From 52c56aff1696cb1418c2d8c370c811f897b0b45d Mon Sep 17 00:00:00 2001 From: Venexia Walker Date: Fri, 3 Feb 2023 17:34:46 +0000 Subject: [PATCH] Further tidying and setup for prevax_extf --- analysis/active_analyses.R | 2 +- analysis/codelists.py | 7 + analysis/common_variables.py | 48 +- analysis/create_project_actions.R | 105 +- analysis/{model => }/fn-check_vitals.R | 0 analysis/{model => }/make_model_input.R | 93 +- analysis/{model => }/make_model_output.R | 0 .../{preprocess => }/modify_dummy_vax_data.R | 0 analysis/prelim.R | 3 +- analysis/preprocess/Stage1_data_cleaning.R | 374 -- analysis/{preprocess => }/preprocess_data.R | 0 analysis/stage1_data_cleaning.R | 404 ++ analysis/study_definition_prevax_extf.py | 89 + lib/active_analyses.rds | Bin 5052 -> 4916 bytes project.yaml | 3565 ++++++++--------- 15 files changed, 2305 insertions(+), 2385 deletions(-) rename analysis/{model => }/fn-check_vitals.R (100%) rename analysis/{model => }/make_model_input.R (80%) rename analysis/{model => }/make_model_output.R (100%) rename analysis/{preprocess => }/modify_dummy_vax_data.R (100%) delete mode 100644 analysis/preprocess/Stage1_data_cleaning.R rename analysis/{preprocess => }/preprocess_data.R (100%) create mode 100644 analysis/stage1_data_cleaning.R create mode 100644 analysis/study_definition_prevax_extf.py diff --git a/analysis/active_analyses.R b/analysis/active_analyses.R index ec80638e..0c3f63dc 100644 --- a/analysis/active_analyses.R +++ b/analysis/active_analyses.R @@ -489,7 +489,7 @@ tmp <- df[df$cohort=="prevax" & "sub_covid_nonhospitalised") | df$outcome %in% outcomes_runall),] -tmp$outcome <- paste0(tmp$outcome,"_extf") +tmp$cohort <- paste0(tmp$cohort,"_extf") tmp$study_stop <- "2021-12-14" tmp$cut_points <- "28;197;365;714" diff --git a/analysis/codelists.py b/analysis/codelists.py index a2a060e9..cf7c97df 100644 --- a/analysis/codelists.py +++ b/analysis/codelists.py @@ -598,6 +598,13 @@ self_harm_15plus_snomed_clinical ) +# OCD ICD10 +ocd_icd10 = codelist_from_csv( + "codelists/user-kurttaylor-ocd_icd10.csv", + system="icd10", + column="code", +) + # Suicide suicide_icd10 = codelist_from_csv( "codelists/user-hjforbes-suicide-icd-10.csv", diff --git a/analysis/common_variables.py b/analysis/common_variables.py index 215dbf73..d31c8740 100644 --- a/analysis/common_variables.py +++ b/analysis/common_variables.py @@ -194,7 +194,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_depression_snomed=patients.with_these_clinical_events( depression_snomed_clinical, returning="date", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -208,7 +208,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_depression_hes=patients.admitted_to_hospital( returning="date_admitted", with_these_diagnoses=depression_icd10, - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -222,7 +222,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_depression_death=patients.with_these_codes_on_death_certificate( depression_icd10, returning="date_of_death", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], match_only_underlying_cause=True, date_format="YYYY-MM-DD", return_expectations={ @@ -243,7 +243,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_anxiety_general_snomed=patients.with_these_clinical_events( anxiety_general_snomed_clinical, returning="date", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -257,7 +257,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_anxiety_general_hes=patients.admitted_to_hospital( returning="date_admitted", with_these_diagnoses=anxiety_icd10, - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -271,7 +271,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_anxiety_general_death=patients.with_these_codes_on_death_certificate( anxiety_icd10, returning="date_of_death", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], match_only_underlying_cause=True, date_format="YYYY-MM-DD", return_expectations={ @@ -292,7 +292,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_anxiety_ptsd_snomed=patients.with_these_clinical_events( anxiety_ptsd_snomed_clinical, returning="date", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -306,7 +306,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_anxiety_ptsd_hes=patients.admitted_to_hospital( returning="date_admitted", with_these_diagnoses=ptsd_icd10, - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -320,7 +320,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_anxiety_ptsd_death=patients.with_these_codes_on_death_certificate( ptsd_icd10, returning="date_of_death", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], match_only_underlying_cause=True, date_format="YYYY-MM-DD", return_expectations={ @@ -341,7 +341,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_eating_disorders_snomed=patients.with_these_clinical_events( eating_disorders_snomed_clinical, returning="date", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -355,7 +355,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_eating_disorders_hes=patients.admitted_to_hospital( returning="date_admitted", with_these_diagnoses=eating_disorder_icd10, - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -369,7 +369,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_eating_disorders_death=patients.with_these_codes_on_death_certificate( eating_disorder_icd10, returning="date_of_death", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], match_only_underlying_cause=True, date_format="YYYY-MM-DD", return_expectations={ @@ -390,7 +390,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_serious_mental_illness_snomed=patients.with_these_clinical_events( serious_mental_illness_snomed_clinical, returning="date", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -404,7 +404,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_serious_mental_illness_hes=patients.admitted_to_hospital( returning="date_admitted", with_these_diagnoses=serious_mental_illness_icd10, - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -418,7 +418,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_serious_mental_illness_death=patients.with_these_codes_on_death_certificate( serious_mental_illness_icd10, returning="date_of_death", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], match_only_underlying_cause=True, date_format="YYYY-MM-DD", return_expectations={ @@ -439,7 +439,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_self_harm_snomed=patients.with_these_clinical_events( self_harm_15_10_combined_snomed, returning="date", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -453,7 +453,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_self_harm_hes=patients.admitted_to_hospital( returning="date_admitted", with_these_diagnoses=self_harm_15_10_combined_icd, - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -467,7 +467,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_self_harm_death=patients.with_these_codes_on_death_certificate( self_harm_15_10_combined_icd, returning="date_of_death", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], match_only_underlying_cause=True, date_format="YYYY-MM-DD", return_expectations={ @@ -488,7 +488,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_suicide_hes=patients.admitted_to_hospital( returning="date_admitted", with_these_diagnoses=suicide_icd10, - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -502,7 +502,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_suicide_death=patients.with_these_codes_on_death_certificate( suicide_icd10, returning="date_of_death", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], match_only_underlying_cause=True, date_format="YYYY-MM-DD", return_expectations={ @@ -523,7 +523,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_addiction_snomed=patients.with_these_clinical_events( addiction_snomed_clinical, returning="date", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -537,7 +537,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_addiction_hes=patients.admitted_to_hospital( returning="date_admitted", with_these_diagnoses=opioid_misuse_icd10, - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], date_format="YYYY-MM-DD", find_first_match_in_period=True, return_expectations={ @@ -551,7 +551,7 @@ def generate_common_variables(index_date_variable,end_date_variable): tmp_out_date_addiction_death=patients.with_these_codes_on_death_certificate( opioid_misuse_icd10, returning="date_of_death", - on_or_after=f"{index_date_variable}", + between=[f"{index_date_variable}",f"{end_date_variable}"], match_only_underlying_cause=True, date_format="YYYY-MM-DD", return_expectations={ @@ -1309,4 +1309,4 @@ def generate_common_variables(index_date_variable,end_date_variable): ) - return dynamic_variables \ No newline at end of file + return dynamic_variables diff --git a/analysis/create_project_actions.R b/analysis/create_project_actions.R index 9ec5e815..4a11c6b5 100644 --- a/analysis/create_project_actions.R +++ b/analysis/create_project_actions.R @@ -106,7 +106,7 @@ apply_model_function <- function(name, cohort, analysis, ipw, strata, splice( action( name = glue("make_model_input-{name}"), - run = glue("r:latest analysis/model/make_model_input.R {name}"), + run = glue("r:latest analysis/make_model_input.R {name}"), needs = list("stage1_data_cleaning_all"), highly_sensitive = list( model_input = glue("output/model_input-{name}.rds") @@ -204,6 +204,17 @@ actions_list <- splice( ) ), + comment("Implement study_definition for prevax_extf"), + + action( + name = "generate_study_population_prevax_extf", + run = "cohortextractor:latest generate_cohort --study-definition study_definition_prevax_extf --output-format csv.gz", + needs = list("vax_eligibility_inputs","generate_index_dates"), + highly_sensitive = list( + cohort = glue("output/input_prevax_extf.csv.gz") + ) + ), + comment("Implement study_definition for vax"), action( @@ -230,7 +241,7 @@ actions_list <- splice( action( name = "preprocess_data_prevax", - run = "r:latest analysis/preprocess/preprocess_data.R prevax", + run = "r:latest analysis/preprocess_data.R prevax", needs = list( "generate_index_dates","generate_study_population_prevax"), moderately_sensitive = list( describe = glue("output/describe_input_prevax_stage0.txt"), @@ -242,11 +253,27 @@ actions_list <- splice( ) ), + comment("Preprocess data - prevax_extf"), + + action( + name = "preprocess_data_prevax_extf", + run = "r:latest analysis/preprocess_data.R prevax_extf", + needs = list( "generate_index_dates","generate_study_population_prevax_extf"), + moderately_sensitive = list( + describe = glue("output/describe_input_prevax_extf_stage0.txt"), + describe_venn = glue("output/describe_venn_prevax_extf.txt") + ), + highly_sensitive = list( + cohort = glue("output/input_prevax_extf.rds"), + venn = glue("output/venn_prevax_extf.rds") + ) + ), + comment("Preprocess data - vax"), action( name = "preprocess_data_vax", - run = "r:latest analysis/preprocess/preprocess_data.R vax", + run = "r:latest analysis/preprocess_data.R vax", needs = list("generate_index_dates","generate_study_population_vax"), moderately_sensitive = list( describe = glue("output/describe_input_vax_stage0.txt"), @@ -262,7 +289,7 @@ actions_list <- splice( action( name = "preprocess_data_unvax", - run = "r:latest analysis/preprocess/preprocess_data.R unvax", + run = "r:latest analysis/preprocess_data.R unvax", needs = list("generate_index_dates", "generate_study_population_unvax"), moderately_sensitive = list( describe = glue("output/describe_input_unvax_stage0.txt"), @@ -274,16 +301,16 @@ actions_list <- splice( ) ), - comment("Stage 1 - Data cleaning - all cohorts"), + comment("Data cleaning - all cohorts"), action( name = "stage1_data_cleaning_all", - run = "r:latest analysis/preprocess/Stage1_data_cleaning.R all", - needs = list("preprocess_data_prevax","preprocess_data_vax", "preprocess_data_unvax","vax_eligibility_inputs"), + run = "r:latest analysis/stage1_data_cleaning.R all", + needs = list("preprocess_data_prevax","preprocess_data_prevax_extf","preprocess_data_vax", "preprocess_data_unvax","vax_eligibility_inputs"), moderately_sensitive = list( refactoring = glue("output/meta_data_factors_*.csv"), - QA_rules = glue("output/descriptives/QA_summary_*.csv"), - IE_criteria = glue("output/descriptives/Cohort_flow_*.csv"), + QA_rules = glue("output/QA_summary_*.csv"), + IE_criteria = glue("output/Cohort_flow_*.csv"), histograms = glue("output/numeric_histograms_*.svg") ), highly_sensitive = list( @@ -300,6 +327,15 @@ actions_list <- splice( ) ), + action( + name = glue("describe_file-input_prevax_extf_stage1"), + run = glue("r:latest analysis/describe_file.R input_prevax_extf_stage1 rds"), + needs = list("stage1_data_cleaning_all"), + moderately_sensitive = list( + describe_model_input = glue("output/describe-input_prevax_extf_stage1.txt") + ) + ), + action( name = glue("describe_file-input_vax_stage1"), run = glue("r:latest analysis/describe_file.R input_vax_stage1 rds"), @@ -370,47 +406,18 @@ actions_list <- splice( covariate_threshold = active_analyses$covariate_threshold[x], age_spline = active_analyses$age_spline[x])), recursive = FALSE ) - ), - - comment("Stage 6 - make model output"), + )#, - action( - name = "make_model_output", - run = "r:latest analysis/model/make_model_output.R", - needs = as.list(paste0("cox_ipw-",success$name)), - moderately_sensitive = list( - model_output = glue("output/model_output.csv") - ) - ), - - comment("Temp"), - - action( - name = "cox_ipw-cohort_prevax-main-depression-v0.0.9", - run = "cox-ipw:v0.0.9 --df_input=model_input-cohort_prevax-main-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-depression-v0.0.9.csv", - needs = as.list("make_model_input-cohort_prevax-main-depression"), - moderately_sensitive = list( - model_output = glue("output/model_output-cohort_prevax-main-depression-v0.0.9.csv") - ) - ), - - action( - name = "cox_ipw-cohort_vax-main-depression-v0.0.9", - run = "cox-ipw:v0.0.9 --df_input=model_input-cohort_vax-main-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-depression-v0.0.9", - needs = as.list("make_model_input-cohort_vax-main-depression"), - moderately_sensitive = list( - model_output = glue("output/model_output-cohort_vax-main-depression-v0.0.9.csv") - ) - ), - - action( - name = "cox_ipw-cohort_unvax-main-depression-v0.0.9", - run = "cox-ipw:v0.0.9 --df_input=model_input-cohort_unvax-main-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-depression-v0.0.9", - needs = as.list("make_model_input-cohort_unvax-main-depression"), - moderately_sensitive = list( - model_output = glue("output/model_output-cohort_unvax-main-depression-v0.0.9.csv") - ) - ) + # comment("Stage 6 - make model output"), + # + # action( + # name = "make_model_output", + # run = "r:latest analysis/make_model_output.R", + # needs = as.list(paste0("cox_ipw-",success$name)), + # moderately_sensitive = list( + # model_output = glue("output/model_output.csv") + # ) + # ) ) diff --git a/analysis/model/fn-check_vitals.R b/analysis/fn-check_vitals.R similarity index 100% rename from analysis/model/fn-check_vitals.R rename to analysis/fn-check_vitals.R diff --git a/analysis/model/make_model_input.R b/analysis/make_model_input.R similarity index 80% rename from analysis/model/make_model_input.R rename to analysis/make_model_input.R index 25c5b705..c36f8c3e 100644 --- a/analysis/model/make_model_input.R +++ b/analysis/make_model_input.R @@ -16,7 +16,7 @@ args <- commandArgs(trailingOnly=TRUE) if(length(args)==0){ # name <- "all" # prepare datasets for all active analyses - name <- "cohort_prevax-sub_priorhistory" # prepare datasets for all active analyses whose name contains X + name <- "cohort_prevax-main-addiction" # prepare datasets for all active analyses whose name contains X # name <- "vax-depression-main;vax-depression-sub_covid_hospitalised;vax-depression-sub_covid_nonhospitalised" # prepare datasets for specific active analyses } else { name <- args[[1]] @@ -53,8 +53,6 @@ for (i in 1:nrow(active_analyses)) { # Restrict to required variables ----------------------------------------------- print('Restrict to required variables') - history_components <- colnames(input)[grepl("cov_bin_recent",colnames(input)) | grepl("cov_bin_history",colnames(input))] - input <- input[,unique(c("patient_id", "index_date", "end_date", @@ -66,11 +64,10 @@ for (i in 1:nrow(active_analyses)) { "sub_bin_covid19_confirmed_history", "cov_cat_sex", "cov_num_age", - "cov_cat_ethnicity", - history_components))] + "cov_cat_ethnicity"))] - # Remove outcomes outside of follow-up time ------------------------------------ + # Remove outcomes outside of follow-up time ---------------------------------- print('Remove outcomes outside of follow-up time') input <- dplyr::rename(input, @@ -89,48 +86,48 @@ for (i in 1:nrow(active_analyses)) { dplyr::rowwise() %>% dplyr::mutate(end_date = min(end_date, out_date, na.rm = TRUE)) - # Make three level history covariates ---------------------------------------- - print('Make three level history covariates') - - input$cov_cat_priorhistory_depression <- dplyr::case_when( - input$cov_bin_history_depression==TRUE & input$cov_bin_recent_depression==TRUE ~ "recent", - input$cov_bin_history_depression==TRUE & input$cov_bin_recent_depression==FALSE ~ "notrecent", - input$cov_bin_history_depression==FALSE & input$cov_bin_recent_depression==TRUE ~ "recent", - input$cov_bin_history_depression==FALSE & input$cov_bin_recent_depression==FALSE ~ "none") - input[,c("cov_bin_history_depression","cov_bin_recent_depression")] <- NULL - input$cov_cat_priorhistory_depression <- as.factor(input$cov_cat_priorhistory_depression) - - input$cov_cat_priorhistory_anxiety_general <- dplyr::case_when( - input$cov_bin_history_anxiety==TRUE & input$cov_bin_recent_anxiety==TRUE ~ "recent", - input$cov_bin_history_anxiety==TRUE & input$cov_bin_recent_anxiety==FALSE ~ "notrecent", - input$cov_bin_history_anxiety==FALSE & input$cov_bin_recent_anxiety==TRUE ~ "recent", - input$cov_bin_history_anxiety==FALSE & input$cov_bin_recent_anxiety==FALSE ~ "none") - input[,c("cov_bin_history_anxiety","cov_bin_recent_anxiety")] <- NULL - input$cov_cat_priorhistory_anxiety_general <- as.factor(input$cov_cat_priorhistory_anxiety_general) - - input$cov_cat_priorhistory_eating_disorders <- dplyr::case_when( - input$cov_bin_history_eating_disorders==TRUE & input$cov_bin_recent_eating_disorders==TRUE ~ "recent", - input$cov_bin_history_eating_disorders==TRUE & input$cov_bin_recent_eating_disorders==FALSE ~ "notrecent", - input$cov_bin_history_eating_disorders==FALSE & input$cov_bin_recent_eating_disorders==TRUE ~ "recent", - input$cov_bin_history_eating_disorders==FALSE & input$cov_bin_recent_eating_disorders==FALSE ~ "none") - input[,c("cov_bin_history_eating_disorders","cov_bin_recent_eating_disorders")] <- NULL - input$cov_cat_priorhistory_eating_disorders <- as.factor(input$cov_cat_priorhistory_eating_disorders) - - input$cov_cat_priorhistory_serious_mental_illness <- dplyr::case_when( - input$cov_bin_history_serious_mental_illness==TRUE & input$cov_bin_recent_serious_mental_illness==TRUE ~ "recent", - input$cov_bin_history_serious_mental_illness==TRUE & input$cov_bin_recent_serious_mental_illness==FALSE ~ "notrecent", - input$cov_bin_history_serious_mental_illness==FALSE & input$cov_bin_recent_serious_mental_illness==TRUE ~ "recent", - input$cov_bin_history_serious_mental_illness==FALSE & input$cov_bin_recent_serious_mental_illness==FALSE ~ "none") - input[,c("cov_bin_history_serious_mental_illness","cov_bin_recent_serious_mental_illness")] <- NULL - input$cov_cat_priorhistory_serious_mental_illness <- as.factor(input$cov_cat_priorhistory_serious_mental_illness) - - input$cov_cat_priorhistory_self_harm <- dplyr::case_when( - input$cov_bin_history_self_harm==TRUE & input$cov_bin_recent_self_harm==TRUE ~ "recent", - input$cov_bin_history_self_harm==TRUE & input$cov_bin_recent_self_harm==FALSE ~ "notrecent", - input$cov_bin_history_self_harm==FALSE & input$cov_bin_recent_self_harm==TRUE ~ "recent", - input$cov_bin_history_self_harm==FALSE & input$cov_bin_recent_self_harm==FALSE ~ "none") - input[,c("cov_bin_history_self_harm","cov_bin_recent_self_harm")] <- NULL - input$cov_cat_priorhistory_self_harm <- as.factor(input$cov_cat_priorhistory_self_harm) + # # Make three level history covariates ---------------------------------------- + # print('Make three level history covariates') + # + # input$cov_cat_priorhistory_depression <- dplyr::case_when( + # input$cov_bin_history_depression==TRUE & input$cov_bin_recent_depression==TRUE ~ "recent", + # input$cov_bin_history_depression==TRUE & input$cov_bin_recent_depression==FALSE ~ "notrecent", + # input$cov_bin_history_depression==FALSE & input$cov_bin_recent_depression==TRUE ~ "recent", + # input$cov_bin_history_depression==FALSE & input$cov_bin_recent_depression==FALSE ~ "none") + # input[,c("cov_bin_history_depression","cov_bin_recent_depression")] <- NULL + # input$cov_cat_priorhistory_depression <- as.factor(input$cov_cat_priorhistory_depression) + # + # input$cov_cat_priorhistory_anxiety_general <- dplyr::case_when( + # input$cov_bin_history_anxiety==TRUE & input$cov_bin_recent_anxiety==TRUE ~ "recent", + # input$cov_bin_history_anxiety==TRUE & input$cov_bin_recent_anxiety==FALSE ~ "notrecent", + # input$cov_bin_history_anxiety==FALSE & input$cov_bin_recent_anxiety==TRUE ~ "recent", + # input$cov_bin_history_anxiety==FALSE & input$cov_bin_recent_anxiety==FALSE ~ "none") + # input[,c("cov_bin_history_anxiety","cov_bin_recent_anxiety")] <- NULL + # input$cov_cat_priorhistory_anxiety_general <- as.factor(input$cov_cat_priorhistory_anxiety_general) + # + # input$cov_cat_priorhistory_eating_disorders <- dplyr::case_when( + # input$cov_bin_history_eating_disorders==TRUE & input$cov_bin_recent_eating_disorders==TRUE ~ "recent", + # input$cov_bin_history_eating_disorders==TRUE & input$cov_bin_recent_eating_disorders==FALSE ~ "notrecent", + # input$cov_bin_history_eating_disorders==FALSE & input$cov_bin_recent_eating_disorders==TRUE ~ "recent", + # input$cov_bin_history_eating_disorders==FALSE & input$cov_bin_recent_eating_disorders==FALSE ~ "none") + # input[,c("cov_bin_history_eating_disorders","cov_bin_recent_eating_disorders")] <- NULL + # input$cov_cat_priorhistory_eating_disorders <- as.factor(input$cov_cat_priorhistory_eating_disorders) + # + # input$cov_cat_priorhistory_serious_mental_illness <- dplyr::case_when( + # input$cov_bin_history_serious_mental_illness==TRUE & input$cov_bin_recent_serious_mental_illness==TRUE ~ "recent", + # input$cov_bin_history_serious_mental_illness==TRUE & input$cov_bin_recent_serious_mental_illness==FALSE ~ "notrecent", + # input$cov_bin_history_serious_mental_illness==FALSE & input$cov_bin_recent_serious_mental_illness==TRUE ~ "recent", + # input$cov_bin_history_serious_mental_illness==FALSE & input$cov_bin_recent_serious_mental_illness==FALSE ~ "none") + # input[,c("cov_bin_history_serious_mental_illness","cov_bin_recent_serious_mental_illness")] <- NULL + # input$cov_cat_priorhistory_serious_mental_illness <- as.factor(input$cov_cat_priorhistory_serious_mental_illness) + # + # input$cov_cat_priorhistory_self_harm <- dplyr::case_when( + # input$cov_bin_history_self_harm==TRUE & input$cov_bin_recent_self_harm==TRUE ~ "recent", + # input$cov_bin_history_self_harm==TRUE & input$cov_bin_recent_self_harm==FALSE ~ "notrecent", + # input$cov_bin_history_self_harm==FALSE & input$cov_bin_recent_self_harm==TRUE ~ "recent", + # input$cov_bin_history_self_harm==FALSE & input$cov_bin_recent_self_harm==FALSE ~ "none") + # input[,c("cov_bin_history_self_harm","cov_bin_recent_self_harm")] <- NULL + # input$cov_cat_priorhistory_self_harm <- as.factor(input$cov_cat_priorhistory_self_harm) # Make model input: main ------------------------------------------------------- diff --git a/analysis/model/make_model_output.R b/analysis/make_model_output.R similarity index 100% rename from analysis/model/make_model_output.R rename to analysis/make_model_output.R diff --git a/analysis/preprocess/modify_dummy_vax_data.R b/analysis/modify_dummy_vax_data.R similarity index 100% rename from analysis/preprocess/modify_dummy_vax_data.R rename to analysis/modify_dummy_vax_data.R diff --git a/analysis/prelim.R b/analysis/prelim.R index d09f4b8a..770887fb 100644 --- a/analysis/prelim.R +++ b/analysis/prelim.R @@ -26,7 +26,8 @@ prelim_data <- prelim_data %>% index_unvax = max(c(vax_date_eligible_offset, delta_date), na.rm=T), end_vax = min(c(death_date, delta_end_date), na.rm=T), end_unvax = min(c(death_date, delta_end_date), na.rm=T), - end_prevax = min(c(vax_date_eligible,death_date, vax_date_covid_1, all_eligible_date), na.rm=T)) + end_prevax = min(c(vax_date_eligible,death_date, vax_date_covid_1, all_eligible_date), na.rm=T), + end_prevax_exf = min(c(death_date, vax_date_covid_1, na.rm=T))) #Write data to csv file diff --git a/analysis/preprocess/Stage1_data_cleaning.R b/analysis/preprocess/Stage1_data_cleaning.R deleted file mode 100644 index dadf1d52..00000000 --- a/analysis/preprocess/Stage1_data_cleaning.R +++ /dev/null @@ -1,374 +0,0 @@ -## ============================================================================= -#Based on script in vaccinated repo -## ============================================================================= - - -############################################### -# 0. Load relevant libraries and read in data # -############################################### - -#Load libraries using pacman -pacman::p_load(dplyr,tictoc,readr,stringr,tidyr,ggplot2,jsonlite,here,arrow) - -#clear memory -rm(list=ls()) - -# Get dataset for either the vaccinated or electively unvaccinated subcohort -# Specify command arguments ---------------------------------------------------- - -args <- commandArgs(trailingOnly=TRUE) - -if(length(args)==0){ - # use for interactive testing - cohort_name <- "all" - -} else { - cohort_name <- args[[1]] -} - -fs::dir_create(here::here("output", "not-for-review")) -fs::dir_create(here::here("output", "review", "descriptives")) - -#json file containing vax study dates -study_dates <- fromJSON("output/study_dates.json") -#vaccinattion program start date -vax_start_date<-as.Date(study_dates$vax1_earliest, format="%Y-%m-%d") - -#reference date for mixed vaccine products -mixed_vax_threshold<-as.Date("2021-05-07") -#read date variables from json file -start_date_delta = as.Date(study_dates$delta_date, format="%Y-%m-%d") -end_date_delta = as.Date(study_dates$omicron_date, format="%Y-%m-%d") - -stage1 <- function(cohort_name){ - - input <- read_rds(file.path("output", paste0("input_",cohort_name,".rds"))) - print(paste0(cohort_name, " ", nrow(input), " rows in the input file")) - -#Rename the index_date_vax/unvax/prevax to index_date - input<- input %>% - rename(index_date=!!sym(paste0("index_date_",cohort_name))) %>% - rename(end_date = !!sym(paste0("end_date_",cohort_name))) - - - - # NOTE: no censoring of end date for death/event at this stage - - ###################################################### - # 1. Prepare all variables (re-factoring, re-typing) # - ###################################################### - - # Handle missing values - - input$cov_cat_smoking_status <- replace(input$cov_cat_smoking_status, is.na(input$cov_cat_smoking_status),"M") - input <- input %>% mutate(cov_cat_region = as.character(cov_cat_region)) %>% - mutate(cov_cat_region = replace_na(cov_cat_region, "Missing")) %>% - mutate(cov_cat_region = as.factor(cov_cat_region)) - - # For categorical factors, specify references - - cat_factors <- colnames(input)[grepl("_cat_",colnames(input))] - input[,cat_factors] <- lapply(input[,cat_factors], function(x) factor(x, ordered = FALSE)) - - ## sub_cat_covid19_hospital - input$sub_cat_covid19_hospital <- ordered(input$sub_cat_covid19_hospital, levels = c("non_hospitalised","hospitalised","no_infection")) - - ## cov_cat_ethnicity - levels(input$cov_cat_ethnicity) <- list("Missing" = "0", "White" = "1", "Mixed" = "2", "South Asian" = "3", "Black" = "4", "Other" = "5") - input$cov_cat_ethnicity <- ordered(input$cov_cat_ethnicity, levels = c("White","Mixed","South Asian","Black","Other","Missing")) - - ## cov_cat_deprivation - levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==1 | levels(input$cov_cat_deprivation)==2] <-"1-2 (most deprived)" - levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==3 | levels(input$cov_cat_deprivation)==4] <-"3-4" - levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==5 | levels(input$cov_cat_deprivation)==6] <-"5-6" - levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==7 | levels(input$cov_cat_deprivation)==8] <-"7-8" - levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==9 | levels(input$cov_cat_deprivation)==10] <-"9-10 (least deprived)" - input$cov_cat_deprivation <- ordered(input$cov_cat_deprivation, levels = c("1-2 (most deprived)","3-4","5-6","7-8","9-10 (least deprived)")) - - ## cov_cat_region - input$cov_cat_region <- relevel(input$cov_cat_region, ref = "East") - - ## cov_cat_smoking_status - levels(input$cov_cat_smoking_status) <- list("Ever smoker" = "E", "Missing" = "M", "Never smoker" = "N", "Current smoker" = "S") - input$cov_cat_smoking_status <- ordered(input$cov_cat_smoking_status, levels = c("Never smoker","Ever smoker","Current smoker","Missing")) - - ## cov_cat_bmi - - input$cov_cat_bmi_groups <- ordered(input$cov_cat_bmi_groups, levels = c("Healthy_weight", "Underweight", "Overweight", "Obese", "Missing")) - - ## cov_cat_sex - levels(input$cov_cat_sex) <- list("Female" = "F", "Male" = "M") - input$cov_cat_sex <- relevel(input$cov_cat_sex, ref = "Female") - - ## vax_cat_jcvi_group - input$vax_cat_jcvi_group <- ordered(input$vax_cat_jcvi_group, levels = c("12","11","10","09","08","07","06","05","04","03","02","01","99")) - - ## vax_cat_product_* - vax_cat_product_factors <- colnames(input)[grepl("vax_cat_product_",colnames(input))] - input[,vax_cat_product_factors] <- lapply(input[,vax_cat_product_factors], function(x) ordered(x, levels = c("Pfizer","AstraZeneca","Moderna"))) - - ## Set reference level for binary covariates - bin_factors <- colnames(input)[grepl("cov_bin_",colnames(input))] - input[,bin_factors] <- lapply(input[,bin_factors], function(x) factor(x, levels = c("FALSE","TRUE"))) - - - ##################### - # 2. Apply QA rules # - ##################### - - #Rule 1: Year of birth is after year of death or patient only has year of death - input$rule1=NA - input$rule1=((input$qa_num_birth_year > (format(input$death_date, format="%Y")) & is.na(input$qa_num_birth_year)== FALSE & is.na(input$death_date) == FALSE)|(is.na(input$qa_num_birth_year)== TRUE & is.na(input$death_date) == FALSE)) - - #Rule 2: Year of birth predates NHS established year or year of birth exceeds current date - input$rule2=NA - input$rule2=((input$qa_num_birth_year <1793 |(input$qa_num_birth_year >format(Sys.Date(),"%Y"))) & is.na(input$qa_num_birth_year) == FALSE) - - #Rule 3: Date of death is NULL or invalid (on or before 1/1/1900 or after current date) - input$rule3=NA - input$rule3=((input$death_date <=as.Date(study_dates$earliest_expec)|input$death_date > format(Sys.Date(),"%Y-%m-%d")) & is.na(input$death_date) == FALSE) - - #Rule 4: Pregnancy/birth codes for men - input$rule4=NA - input$rule4=(input$qa_bin_pregnancy == TRUE & input$cov_cat_sex=="Male") - - #Rule 5: HRT or COCP meds for men - input$rule5=NA - input$rule5=((input$cov_cat_sex=="Male" & input$cov_bin_hormone_replacement_therapy==TRUE)|(input$cov_cat_sex=="Male" & input$cov_bin_combined_oral_contraceptive_pill==TRUE)) - - #Rule 6: Prostate cancer codes for women - input$rule6=NA - input$rule6=(input$qa_bin_prostate_cancer == TRUE & input$cov_cat_sex=="Female") - - #Remove rows that are TRUE for at least one rule - input_QA=input%>%filter(rule1==FALSE & rule2==FALSE & rule3==FALSE & rule4==FALSE & rule5==FALSE & rule6==FALSE) - input_QA=input_QA %>% select(-c(rule1,rule2,rule3,rule4,rule5,rule6)) - # View(input_QA) - - #Save QA'd input as .rds - #saveRDS(QA_summary,file = "output/QA_input.rds") - - #QA summary - QA_summary <- data.frame(rule = character(), - n_exclude = numeric()) - - QA_summary[nrow(QA_summary)+1,] <- c("Rule 1: Year of birth is after year of death or patient only has year of death", - nrow(input%>%filter(rule1==T))) - - QA_summary[nrow(QA_summary)+1,] <- c("Rule 2: Year of birth predates NHS established year or year of birth exceeds current date", - nrow(input%>%filter(rule2==T))) - - QA_summary[nrow(QA_summary)+1,] <- c("Rule 3: Date of death is NULL or invalid (on or before 1/1/1900 or after current date)", - nrow(input%>%filter(rule3==T))) - - QA_summary[nrow(QA_summary)+1,] <- c("Rule 4: Pregnancy/birth codes for men", - nrow(input%>%filter(rule4==T))) - - QA_summary[nrow(QA_summary)+1,] <- c("Rule 5: HRT or COCP meds for men", - nrow(input%>%filter(rule5==T))) - - QA_summary[nrow(QA_summary)+1,] <- c("Rule 6: Prostate cancer codes for women", - nrow(input%>%filter(rule6==T))) - - QA_summary[nrow(QA_summary)+1,] <- c("Total excluded from QA", - nrow(input)-nrow(input_QA)) - - #Save Qa summary as .csv - write.csv(QA_summary, file = file.path("output/review/descriptives", paste0("QA_summary_",cohort_name, ".csv")) , row.names=F) - - # Remove QA variables from dataset - input <- input_QA[ , !names(input_QA) %in% c("qa_num_birth_year", "qa_bin_pregnancy", "qa_bin_prostate_cancer")] - - print(paste0(cohort_name, " ", nrow(input), " rows in the input file after QA")) - - ######################################### - # 3. Apply exclusion/inclusion criteria # - ######################################### - # (Differentiate criteria for the two sub-cohorts) - - # Define the cohort flow - cohort_flow <- data.frame(N = numeric(), - N_removed = numeric(), - Description = character(), - stringsAsFactors = FALSE) - cohort_flow[nrow(cohort_flow)+1,] <- c(as.numeric(as.numeric(nrow(input)) + as.numeric(QA_summary[nrow(QA_summary),"n_exclude"])), 0, "Study defined sample size before QA checks") - - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input), as.numeric(QA_summary[nrow(QA_summary),"n_exclude"]) ,"Study defined sample size after QA checks") - - #----------------------------------------------------------------# - # 3.a. Apply the 6 common criteria applicable to both sub-cohort # - #----------------------------------------------------------------# - - #Inclusion criteria 1: Alive on the first day of follow up - input <- input %>% filter(index_date < death_date | is.na(death_date)) - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 1 (Inclusion): Alive on the first day of follow up") # Feed into the cohort flow - - #Inclusion criteria 2: Known age between 18 and 110 on 01/06/2021 - input <- subset(input, input$cov_num_age >= 18) # Subset input if age between 18 and 110 on 01/06/2021. - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 2a (Inclusion): Aged 18 and over on index date") # Feed into the cohort flow - - input <- subset(input, input$cov_num_age <= 110) # Subset input if age between 18 and 110 on 01/06/2021. - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 2b (Inclusion): Aged 110 and under on index date") # Feed into the cohort flow - - #Inclusion criteria 3: Known sex - input <- input[!is.na(input$cov_cat_sex),] # removes NAs, if any - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 3 (Inclusion): Known sex") - - #Inclusion criteria 4: Known deprivation - input <- input[!is.na(input$cov_cat_deprivation),] # removes NAs, if any - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 4 (Inclusion): Known deprivation") - - #Inclusion criteria 5: Registered in an English GP with TPP software for at least 6 months prior to the study start date - input <- subset(input, input$has_follow_up_previous_6months == TRUE) - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 5 (Inclusion): Registered in an English GP with TPP software for at least 6 months prior to the study start date") - - #Inclusion criteria 6: Not deregistered - input <- input %>% - filter(is.na(dereg_date)) - #cohort_flow <- rbind(cohort_flow,c(nrow(input),as.numeric(cohort_flow[(nrow(input)-1),1]) - nrow(input))) - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 6 (Exclusion): Not deregistered from all support practices between index and end of study date") - - #Inclusion criteria 7: Known region - input <- input %>% mutate(cov_cat_region = as.character(cov_cat_region)) %>% - filter(cov_cat_region != "Missing")%>% - mutate(cov_cat_region = as.factor(cov_cat_region)) - - input$cov_cat_region <- relevel(input$cov_cat_region, ref = "East") - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 7 (Inclusion): Known region") - - # A simple check if factor reference level has changed - describe_vars <- tidyselect::vars_select(names(input), contains(c('_cat_', 'cov_bin','cov_cat','qa_bin','exp_cat','vax_cat', 'step'), ignore.case = TRUE)) - meta_data_factors <- lapply(input[,c(describe_vars)], table) - - - - #-------------------------------------------------# - # 3.b. Apply criteria specific to each sub-cohort # - #-------------------------------------------------# - - if (cohort_name == "vax") { - - #Exclusion criteria 8: Do not have a record of two vaccination doses prior to the study end date - input$vax_gap <- input$vax_date_covid_2 - input$vax_date_covid_1 #Determine the vaccination gap in days : gap is NA if any vaccine date is missing - input <- input[!is.na(input$vax_gap),] # Subset the fully vaccinated group - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 8 (Exclusion): No record of two vaccination doses prior to the study end date") # Feed into the cohort flow - - #Exclusion criteria 9: Received a vaccination prior to 08-12-2020 (i.e., the start of the vaccination program) - input <- subset(input, input$vax_date_covid_1 >= vax_start_date&input$vax_date_covid_2 >= vax_start_date) - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 9 (Exclusion): Recorded vaccination prior to the start date of vaccination program") - - #Exclusion criteria 10: Received a second dose vaccination before their first dose vaccination - input <- subset(input, input$vax_gap >= 0) # Keep those with positive vaccination gap - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 10 (Exclusion): Second dose vaccination recorded before the first dose vaccination") - - #Exclusion criteria 11: Received a second dose vaccination less than three weeks after their first dose - input <- subset(input, input$vax_gap >= 21) # Keep those with at least 3 weeks vaccination gap - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 11 (Exclusion): Second dose vaccination recorded less than three weeks after the first dose") - - #Exclusion criteria 12: Mixed vaccine products received before 07-05-2021 - # Trick to run the mixed vaccine code on dummy data with limited levels -> To ensure that the levels are the same in vax_cat_product variables - - input <- input %>% - mutate(AZ_date = ifelse(vax_date_AstraZeneca_1 < mixed_vax_threshold, 1, - ifelse(vax_date_AstraZeneca_2 < mixed_vax_threshold, 1, - ifelse(vax_date_AstraZeneca_3 < mixed_vax_threshold, 1, 0)))) %>% - mutate(Moderna_date = ifelse(vax_date_Moderna_1 < mixed_vax_threshold, 1, - ifelse(vax_date_Moderna_2 < mixed_vax_threshold, 1, - ifelse(vax_date_Moderna_3 < mixed_vax_threshold, 1, 0)))) %>% - mutate(Pfizer_date = ifelse(vax_date_Pfizer_1 < mixed_vax_threshold, 1, - ifelse(vax_date_Pfizer_2 < mixed_vax_threshold, 1, - ifelse(vax_date_Pfizer_3 < mixed_vax_threshold, 1, 0)))) %>% - rowwise() %>% - mutate(vax_mixed = sum(across(c("AZ_date", "Moderna_date", "Pfizer_date")), na.rm = T)) %>% - dplyr::filter(vax_mixed < 2) - - - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 12 (Exclusion): Received mixed vaccine products before 07-05-2021") - - #Inclusions criteria 13: Index date is before cohort end date - will remove anyone who is not fully vaccinated by the cohort end date - input <- input %>% filter (!is.na(index_date) & index_date <= end_date & index_date >= start_date_delta) - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 13 (Inclusion): Patient index date is within the study start and end dates i.e patient is fully vaccinated before the study end date") - - - } else if (cohort_name == "unvax"){ - - - #Exclusion criteria 8: Have a record of one or more vaccination prior index date - # i.e. Have a record of a first vaccination prior index date (no more vax 2 and 3 variables available in this dataset) - #a.Determine the vaccination status on index start date - input$prior_vax1 <- ifelse(input$vax_date_covid_1 <= input$index_date, 1,0) - input$prior_vax1[is.na(input$prior_vax1)] <- 0 - - input <- subset(input, input$prior_vax1 == 0) #Exclude people with prior vaccination - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[9,1]) - nrow(input), "Criteria 8 (Exclusion): Have a record of a first vaccination prior index date") - - #Exclusion criteria 9: Missing JCVI group - input <- subset(input, vax_cat_jcvi_group == "01" | vax_cat_jcvi_group == "02" | vax_cat_jcvi_group == "03" | vax_cat_jcvi_group == "04" | - vax_cat_jcvi_group == "05" | vax_cat_jcvi_group == "06" | vax_cat_jcvi_group == "07" | vax_cat_jcvi_group == "08" | - vax_cat_jcvi_group == "09" | vax_cat_jcvi_group == "10" | vax_cat_jcvi_group == "11" | vax_cat_jcvi_group == "12") - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 9 (Exclusion): Missing or unknown JCVI group") - - #Inclusions criteria 10: Index date is before cohort end date - will remove anyone whose eligibility date + 84 days is after study end date (only those with unknown JCVI group) - input <- input %>% filter (!is.na(index_date) & index_date <= end_date & index_date >= start_date_delta) - cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 10 (Inclusion): Patient index date is within the study start and end dates i.e patients eligibility date + 84 days is before the study end date") - - } - - print(paste0(cohort_name, " " , nrow(input), " rows in the input file after cohort specificinclusion criteria")) - - - - print(paste0(cohort_name, " ", nrow(input), " rows in the input file after common inclusion criteria")) - #-------------------------------------------------# - # 3.c. Apply outcome specific exclusions criteria - #-------------------------------------------------# - ####INSERT OUTCOME SPECIFIC EXCLUSION HERE####### - - - - # NB: write.csv is not feasible to output list with uneven length - sink(file = file.path("output/not-for-review", paste0("meta_data_factors_",cohort_name, ".csv"))) - print(meta_data_factors) - sink() - #----------------------# - # 3.d. Create csv file # - #----------------------# - write.csv(cohort_flow, file = file.path("output/review/descriptives", paste0("Cohort_flow_",cohort_name, ".csv")) , row.names=F) - - #--------------------------# - # 3.e. Generate histograms # - #--------------------------# - # generate histograms for numerical variables - - numeric_vars <- input %>% dplyr::select(contains("_num")) - numeric_title <- colnames(numeric_vars) - - svglite::svglite(file = file.path("output/not-for-review/", paste0("numeric_histograms_", cohort_name, "_", ".svg")), width = 15, height = 8) - g <- ggplot(gather(numeric_vars), aes(value)) + - geom_histogram(bins = 10) + - facet_wrap(~key, scales = 'free_x') - print(g) - dev.off() - - #-------------------------------------# - # 4. Create the final stage 1 dataset # - #-------------------------------------# - - # Remove inclusion/exclusion variables from dataset - input <- input[ , !names(input) %in% c("start_alive", "vax_gap", "vax_mixed", "vax_prior_unknown", "prior_vax1")] - - saveRDS(input, file = file.path("output", paste0("input_",cohort_name, "_stage1",".rds"))) - -} - -# Run function using outcome group - - -if (cohort_name == "all") { - stage1("prevax") - stage1("vax") - stage1("unvax") -} else{ - stage1(cohort_name) -} - diff --git a/analysis/preprocess/preprocess_data.R b/analysis/preprocess_data.R similarity index 100% rename from analysis/preprocess/preprocess_data.R rename to analysis/preprocess_data.R diff --git a/analysis/stage1_data_cleaning.R b/analysis/stage1_data_cleaning.R new file mode 100644 index 00000000..fcb094eb --- /dev/null +++ b/analysis/stage1_data_cleaning.R @@ -0,0 +1,404 @@ +# Load libraries --------------------------------------------------------------- + +library(dplyr) +library(tictoc) +library(readr) +library(tidyr) +library(stringr) +library(ggplot2) +library(jsonlite) +library(here) +library(arrow) + +# Specify command arguments ---------------------------------------------------- + +args <- commandArgs(trailingOnly=TRUE) + +if(length(args)==0){ + cohort_name <- "prevax" +} else { + cohort_name <- args[[1]] +} + +# Load json file containing vax study dates ------------------------------------ + +study_dates <- fromJSON("output/study_dates.json") + +# Specify relevant dates ------------------------------------------------------- + +vax_start_date <- as.Date(study_dates$vax1_earliest, format="%Y-%m-%d") +mixed_vax_threshold <- as.Date("2021-05-07") +start_date_delta <- as.Date(study_dates$delta_date, format="%Y-%m-%d") +end_date_delta <- as.Date(study_dates$omicron_date, format="%Y-%m-%d") + +# Define stage 1 function ------------------------------------------------------ + +stage1 <- function(cohort_name) { + + ## Load cohort data ---------------------------------------------------------- + + input <- read_rds(file.path("output", paste0("input_",cohort_name,".rds"))) + print(paste0(cohort_name, " cohort: ", nrow(input), " rows in the input file")) + + ## Rename date variables ----------------------------------------------------- + + input <- input %>% + rename(index_date =!!sym(paste0("index_date_",cohort_name))) %>% + rename(end_date = !!sym(paste0("end_date_",cohort_name))) + + ## Handle missing values ----------------------------------------------------- + + input$cov_cat_smoking_status <- replace(input$cov_cat_smoking_status, + is.na(input$cov_cat_smoking_status), + "M") + + input <- input %>% + mutate(cov_cat_region = as.character(cov_cat_region)) %>% + mutate(cov_cat_region = replace_na(cov_cat_region, "Missing")) %>% + mutate(cov_cat_region = as.factor(cov_cat_region)) + + ## Set reference levels for factors ------------------------------------------ + + cat_factors <- colnames(input)[grepl("_cat_",colnames(input))] + input[,cat_factors] <- lapply(input[,cat_factors], function(x) factor(x, ordered = FALSE)) + + ### Variable: sub_cat_covid19_hospital --------------------------------------- + + input$sub_cat_covid19_hospital <- ordered(input$sub_cat_covid19_hospital, + levels = c("non_hospitalised", + "hospitalised", + "no_infection")) + + ### Variable: cov_cat_ethnicity ---------------------------------------------- + + levels(input$cov_cat_ethnicity) <- list("Missing" = "0", "White" = "1", + "Mixed" = "2", "South Asian" = "3", + "Black" = "4", "Other" = "5") + + input$cov_cat_ethnicity <- ordered(input$cov_cat_ethnicity, + levels = c("White","Mixed", + "South Asian","Black", + "Other","Missing")) + + ### Variable: cov_cat_deprivation -------------------------------------------- + + levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==1 | levels(input$cov_cat_deprivation)==2] <- "1-2 (most deprived)" + levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==3 | levels(input$cov_cat_deprivation)==4] <- "3-4" + levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==5 | levels(input$cov_cat_deprivation)==6] <- "5-6" + levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==7 | levels(input$cov_cat_deprivation)==8] <- "7-8" + levels(input$cov_cat_deprivation)[levels(input$cov_cat_deprivation)==9 | levels(input$cov_cat_deprivation)==10] <- "9-10 (least deprived)" + + input$cov_cat_deprivation <- ordered(input$cov_cat_deprivation, + levels = c("1-2 (most deprived)","3-4","5-6","7-8","9-10 (least deprived)")) + + ### Variable: cov_cat_region ------------------------------------------------- + + input$cov_cat_region <- relevel(input$cov_cat_region, ref = "East") + + ### Variable: cov_cat_smoking_status ----------------------------------------- + + levels(input$cov_cat_smoking_status) <- list("Ever smoker" = "E", "Missing" = "M", "Never smoker" = "N", "Current smoker" = "S") + input$cov_cat_smoking_status <- ordered(input$cov_cat_smoking_status, levels = c("Never smoker","Ever smoker","Current smoker","Missing")) + + ### Variable: cov_cat_sex ---------------------------------------------------- + + levels(input$cov_cat_sex) <- list("Female" = "F", "Male" = "M") + + input$cov_cat_sex <- relevel(input$cov_cat_sex, ref = "Female") + + ### Variable: vax_cat_jcvi_group --------------------------------------------- + + input$vax_cat_jcvi_group <- ordered(input$vax_cat_jcvi_group, + levels = c("12","11","10", + "09","08","07", + "06","05","04", + "03","02","01","99")) + + ### Variable: vax_cat_product_* --------------------------------------------- + + vax_cat_product_factors <- colnames(input)[grepl("vax_cat_product_",colnames(input))] + + input[,vax_cat_product_factors] <- lapply(input[,vax_cat_product_factors], + function(x) ordered(x, levels = c("Pfizer","AstraZeneca","Moderna"))) + + ## Set reference level for binaries ------------------------------------------ + + bin_factors <- colnames(input)[grepl("cov_bin_",colnames(input))] + + input[,bin_factors] <- lapply(input[,bin_factors], + function(x) factor(x, levels = c("FALSE","TRUE"))) + + + ## Apply QA rules ------------------------------------------------------------ + + ### Rule 1: Year of birth is after year of death or patient only has year of death + + input$rule1 <- NA + input$rule1 <- ((input$qa_num_birth_year > (format(input$death_date, format="%Y")) & + is.na(input$qa_num_birth_year)== FALSE & is.na(input$death_date) == FALSE) | + (is.na(input$qa_num_birth_year)== TRUE & is.na(input$death_date) == FALSE)) + + ### Rule 2: Year of birth is before 1793 or year of birth exceeds current date + input$rule2 <- NA + input$rule2 <- ((input$qa_num_birth_year < 1793 | + (input$qa_num_birth_year >format(Sys.Date(),"%Y"))) & + is.na(input$qa_num_birth_year) == FALSE) + + ### Rule 3: Date of death is NULL or invalid (on or before 1/1/1900 or after current date) + + input$rule3 <- NA + input$rule3 <- ((input$death_date <= as.Date(study_dates$earliest_expec) | + input$death_date > format(Sys.Date(),"%Y-%m-%d")) & is.na(input$death_date) == FALSE) + + ### Rule 4: Pregnancy/birth codes for men + + input$rule4 <- NA + input$rule4 <- (input$qa_bin_pregnancy == TRUE & input$cov_cat_sex=="Male") + + ### Rule 5: HRT or COCP meds for men + + input$rule5 <- FALSE + # input$rule5 <- NA + # input$rule5 <- ((input$cov_cat_sex=="Male" & input$qa_bin_hrt==TRUE) | + # (input$cov_cat_sex=="Male" & input$qa_bin_cocp==TRUE)) + + ### Rule 6: Prostate cancer codes for women + + input$rule6 <- NA + input$rule6 <- (input$qa_bin_prostate_cancer == TRUE & + input$cov_cat_sex=="Female") + + ## Keep individuals that meet all QA criteria -------------------------------- + + input_QA <- input %>% + filter(rule1==FALSE & + rule2==FALSE & + rule3==FALSE & + rule4==FALSE & + rule5==FALSE & + rule6==FALSE) + + input_QA <- input_QA %>% + select(-c(rule1,rule2,rule3,rule4,rule5,rule6)) + + # Make QA summary ------------------------------------------------------------ + + QA_summary <- data.frame(rule = character(), + n_exclude = numeric()) + + QA_summary[nrow(QA_summary)+1,] <- c("Rule 1: Year of birth is after year of death or patient only has year of death", + nrow(input%>%filter(rule1==T))) + + QA_summary[nrow(QA_summary)+1,] <- c("Rule 2: Year of birth predates 1793 or year of birth exceeds current date", + nrow(input%>%filter(rule2==T))) + + QA_summary[nrow(QA_summary)+1,] <- c("Rule 3: Date of death is NULL or invalid (on or before 1/1/1900 or after current date)", + nrow(input%>%filter(rule3==T))) + + QA_summary[nrow(QA_summary)+1,] <- c("Rule 4: Pregnancy/birth codes for men", + nrow(input%>%filter(rule4==T))) + + QA_summary[nrow(QA_summary)+1,] <- c("Rule 5: HRT or COCP meds for men", + nrow(input%>%filter(rule5==T))) + + QA_summary[nrow(QA_summary)+1,] <- c("Rule 6: Prostate cancer codes for women", + nrow(input%>%filter(rule6==T))) + + QA_summary[nrow(QA_summary)+1,] <- c("Total excluded from QA", + nrow(input)-nrow(input_QA)) + + # Save QA summary as .csv ---------------------------------------------------- + + write.csv(QA_summary, + file = paste0("output/QA_summary_",cohort_name,".csv"), + row.names=F) + + # Remove QA variables from dataset ------------------------------------------- + + input <- input_QA[, !names(input_QA) %in% c("qa_num_birth_year", + "qa_bin_pregnancy", + "qa_bin_prostate_cancer")] + + print(paste0(cohort_name, " cohort: ", nrow(input), " rows in the input file after QA")) + + ## Define dataset for cohort flow ------------------------------------------- + + cohort_flow <- data.frame(N = numeric(), + N_removed = numeric(), + Description = character(), + stringsAsFactors = FALSE) + + cohort_flow[nrow(cohort_flow)+1,] <- c(as.numeric(as.numeric(nrow(input)) + as.numeric(QA_summary[nrow(QA_summary),"n_exclude"])), 0, "Study defined sample size before QA checks") + + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input), as.numeric(QA_summary[nrow(QA_summary),"n_exclude"]) ,"Study defined sample size after QA checks") + + ## Apply common inclusion/exclusion criteria --------------------------------- + + ### Inclusion criteria 1: Alive on the first day of follow up ---------------- + + input <- input %>% filter(index_date < death_date | is.na(death_date)) + + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 1 (Inclusion): Alive on the first day of follow up") # Feed into the cohort flow + + ### Inclusion criteria 2: Known age between 18 and 110 on 01/06/2021 --------- + + input <- subset(input, input$cov_num_age >= 18) # Subset input if age between 18 and 110 on 01/06/2021. + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 2a (Inclusion): Aged 18 and over on index date") # Feed into the cohort flow + + input <- subset(input, input$cov_num_age <= 110) # Subset input if age between 18 and 110 on 01/06/2021. + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 2b (Inclusion): Aged 110 and under on index date") # Feed into the cohort flow + + ### Inclusion criteria 3: Known sex ------------------------------------------ + + input <- input[!is.na(input$cov_cat_sex),] # removes NAs, if any + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 3 (Inclusion): Known sex") + + ### Inclusion criteria 4: Known deprivation ---------------------------------- + + input <- input[!is.na(input$cov_cat_deprivation),] # removes NAs, if any + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 4 (Inclusion): Known deprivation") + + ### Inclusion criteria 5: Registered in an English GP with TPP software ------ + + input <- subset(input, input$has_follow_up_previous_6months == TRUE) + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 5 (Inclusion): Registered in an English GP with TPP software for at least 6 months prior to the study start date") + + ### Inclusion criteria 6: Not deregistered ----------------------------------- + + input <- input %>% + filter(is.na(dereg_date)) + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 6 (Exclusion): Not deregistered from all support practices between index and end of study date") + + ### Inclusion criteria 7: Known region --------------------------------------- + + input <- input %>% mutate(cov_cat_region = as.character(cov_cat_region)) %>% + filter(cov_cat_region != "Missing")%>% + mutate(cov_cat_region = as.factor(cov_cat_region)) + + input$cov_cat_region <- relevel(input$cov_cat_region, ref = "East") + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 7 (Inclusion): Known region") + + ## Check if factor reference levels have changed ----------------------------- + + describe_vars <- tidyselect::vars_select(names(input), contains(c('_cat_', 'cov_bin','cov_cat','qa_bin','exp_cat','vax_cat', 'step'), ignore.case = TRUE)) + meta_data_factors <- lapply(input[,c(describe_vars)], table) + + ## Apply cohort specific inclusion/exclusion criteria ------------------------ + + if (cohort_name == "vax") { + + ### Exclusion criteria 8: Do not have a record of two vaccination doses prior to the study end date + input$vax_gap <- input$vax_date_covid_2 - input$vax_date_covid_1 #Determine the vaccination gap in days : gap is NA if any vaccine date is missing + input <- input[!is.na(input$vax_gap),] # Subset the fully vaccinated group + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 8 (Exclusion): No record of two vaccination doses prior to the study end date") # Feed into the cohort flow + + #Exclusion criteria 9: Received a vaccination prior to 08-12-2020 (i.e., the start of the vaccination program) + input <- subset(input, input$vax_date_covid_1 >= vax_start_date&input$vax_date_covid_2 >= vax_start_date) + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 9 (Exclusion): Recorded vaccination prior to the start date of vaccination program") + + ### Exclusion criteria 10: Received a second dose vaccination before their first dose vaccination + input <- subset(input, input$vax_gap >= 0) # Keep those with positive vaccination gap + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 10 (Exclusion): Second dose vaccination recorded before the first dose vaccination") + + ### Exclusion criteria 11: Received a second dose vaccination less than three weeks after their first dose + input <- subset(input, input$vax_gap >= 21) # Keep those with at least 3 weeks vaccination gap + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 11 (Exclusion): Second dose vaccination recorded less than three weeks after the first dose") + + ### Exclusion criteria 12: Mixed vaccine products received before 07-05-2021 + # Trick to run the mixed vaccine code on dummy data with limited levels -> To ensure that the levels are the same in vax_cat_product variables + input <- input %>% + mutate(AZ_date = ifelse(vax_date_AstraZeneca_1 < mixed_vax_threshold, 1, + ifelse(vax_date_AstraZeneca_2 < mixed_vax_threshold, 1, + ifelse(vax_date_AstraZeneca_3 < mixed_vax_threshold, 1, 0)))) %>% + mutate(Moderna_date = ifelse(vax_date_Moderna_1 < mixed_vax_threshold, 1, + ifelse(vax_date_Moderna_2 < mixed_vax_threshold, 1, + ifelse(vax_date_Moderna_3 < mixed_vax_threshold, 1, 0)))) %>% + mutate(Pfizer_date = ifelse(vax_date_Pfizer_1 < mixed_vax_threshold, 1, + ifelse(vax_date_Pfizer_2 < mixed_vax_threshold, 1, + ifelse(vax_date_Pfizer_3 < mixed_vax_threshold, 1, 0)))) %>% + rowwise() %>% + mutate(vax_mixed = sum(across(c("AZ_date", "Moderna_date", "Pfizer_date")), na.rm = T)) %>% + dplyr::filter(vax_mixed < 2) + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 12 (Exclusion): Received mixed vaccine products before 07-05-2021") + + ### Inclusions criteria 13: Index date is before cohort end date - will remove anyone who is not fully vaccinated by the cohort end date + input <- input %>% filter (!is.na(index_date) & index_date <= end_date & index_date >= start_date_delta) + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 13 (Inclusion): Patient index date is within the study start and end dates i.e patient is fully vaccinated before the study end date") + + } else if (cohort_name == "unvax"){ + + ### Exclusion criteria 8: Have a record of one or more vaccination prior index date + # i.e. Have a record of a first vaccination prior to index date + # (no more vax 2 and 3 variables available in this dataset) + # a.Determine the vaccination status on index start date + input$prior_vax1 <- ifelse(input$vax_date_covid_1 <= input$index_date, 1,0) + input$prior_vax1[is.na(input$prior_vax1)] <- 0 + + input <- subset(input, input$prior_vax1 == 0) # Exclude people with prior vaccination + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[9,1]) - nrow(input), "Criteria 8 (Exclusion): Have a record of a first vaccination prior index date") + + ### Exclusion criteria 9: Missing JCVI group + input <- subset(input, vax_cat_jcvi_group == "01" | vax_cat_jcvi_group == "02" | vax_cat_jcvi_group == "03" | vax_cat_jcvi_group == "04" | + vax_cat_jcvi_group == "05" | vax_cat_jcvi_group == "06" | vax_cat_jcvi_group == "07" | vax_cat_jcvi_group == "08" | + vax_cat_jcvi_group == "09" | vax_cat_jcvi_group == "10" | vax_cat_jcvi_group == "11" | vax_cat_jcvi_group == "12") + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 9 (Exclusion): Missing or unknown JCVI group") + + ### Inclusion criteria 10: Index date is before cohort end date - will remove anyone whose eligibility date + 84 days is after study end date (only those with unknown JCVI group) + input <- input %>% filter (!is.na(index_date) & index_date <= end_date & index_date >= start_date_delta) + cohort_flow[nrow(cohort_flow)+1,] <- c(nrow(input),as.numeric(cohort_flow[nrow(cohort_flow),"N"]) - nrow(input), "Criteria 10 (Inclusion): Patient index date is within the study start and end dates i.e patients eligibility date + 84 days is before the study end date") + + } + + print(paste0(cohort_name, " cohort: " , nrow(input), " rows in the input file after cohort specific inclusion criteria")) + + print(paste0(cohort_name, " cohort: ", nrow(input), " rows in the input file after common inclusion criteria")) + + ## Save meta data factors ---------------------------------------------------- + + sink(file = file.path("output/", paste0("meta_data_factors_",cohort_name, ".csv"))) + print(meta_data_factors) + sink() + + ## Save cohort flow ---------------------------------------------------------- + + write.csv(cohort_flow, + file = paste0("output/Cohort_flow_",cohort_name, ".csv"), + row.names=F) + + ## Generate histograms for numerical variables ------------------------------- + + numeric_vars <- input %>% dplyr::select(contains("_num")) + numeric_title <- colnames(numeric_vars) + + svglite::svglite(file = paste0("output/numeric_histograms_", cohort_name, "_", ".svg"), + width = 15, height = 8) + + g <- ggplot(gather(numeric_vars), aes(value)) + + geom_histogram(bins = 10) + + facet_wrap(~key, scales = 'free_x') + + print(g) + dev.off() + + ## Remove inclusion/exclusion variables from dataset ------------------------- + + input <- input[ , !names(input) %in% c("start_alive", "vax_gap", "vax_mixed", "vax_prior_unknown", "prior_vax1")] + + ## Save final stage 1 dataset ------------------------------------------------ + + saveRDS(input, + file = paste0("output/input_",cohort_name, "_stage1.rds"), + compress = TRUE) + +} + +# Run Stage 1 function for specified cohort ------------------------------------ + +if (cohort_name == "all") { + stage1("prevax") + stage1("prevax_extf") + stage1("vax") + stage1("unvax") +} else{ + stage1(cohort_name) +} \ No newline at end of file diff --git a/analysis/study_definition_prevax_extf.py b/analysis/study_definition_prevax_extf.py new file mode 100644 index 00000000..623bc453 --- /dev/null +++ b/analysis/study_definition_prevax_extf.py @@ -0,0 +1,89 @@ +# Import statements + +## Set seed +import numpy as np +np.random.seed(123456) + +## Cohort extractor +from cohortextractor import ( + StudyDefinition, + patients, + codelist_from_csv, + codelist, + filter_codes_by_category, + combine_codelists, +) + +## Codelists from codelist.py (which pulls them from the codelist folder) +from codelists import * + +## Datetime functions +from datetime import date + +## Study definition helper +import study_definition_helper_functions as helpers +# Specify index date for MH prevax +## Import common variables function +from common_variables import generate_common_variables +( + dynamic_variables +) = generate_common_variables(index_date_variable="index_date_prevax", end_date_variable="end_date_prevax") + +## Variables for deriving JCVI groups +from grouping_variables import ( + study_dates, + jcvi_variables, + start_date, + end_date, + pandemic_start +) + +study = StudyDefinition( + + # Specify study dates + index_date_prevax = patients.with_value_from_file( + f_path = 'output/index_dates.csv.gz', + returning = 'index_prevax', + returning_type = 'date', + date_format = 'YYYY-MM-DD', + ), + end_date_prevax = patients.with_value_from_file( + f_path = 'output/index_dates.csv.gz', + returning = 'end_prevax', + returning_type = 'date', + date_format = 'YYYY-MM-DD', + ), + + # Configure the expectations framework + default_expectations={ + "date": {"earliest": study_dates["earliest_expec"], "latest": "today"}, + "rate": "uniform", + "incidence": 0.5, + }, + + # Define the study population + # NB: all inclusions and exclusions are performed in stage 1 + population = patients.all(), + + # Define sex + # NB: this is required for JCVI variables hence is defined here + cov_cat_sex = patients.with_value_from_file( + f_path = 'output/index_dates.csv.gz', + returning = 'cov_cat_sex', + returning_type = 'str', + ), + + ## Any covid vaccination, identified by target disease + vax_date_covid_1 = patients.with_value_from_file( + f_path = 'output/index_dates.csv.gz', + returning = 'vax_date_covid_1', + returning_type = 'date' + ), + + # Define vaccine eligibility variables + **jcvi_variables, + + # Define common variables (e.g., exposures, outcomes, covariates) that require dynamic dates + **dynamic_variables + +) \ No newline at end of file diff --git a/lib/active_analyses.rds b/lib/active_analyses.rds index c4a62b16a7e509713c7dd828f5998977b4cd8882..fbe962d89f4b7685257377e2c516ced2f25f56bb 100644 GIT binary patch literal 4916 zcmchZXH-+^+J>>>poqdK3XF`XAVNSP^yWbk0Re@~L?Xp8p-T%@AVg$nh9Xr6Md=2H zAYf>rh;(8oLTDi%1VS?)1Og-w4vga&JjWmB$N9cz-RoZ0y5IfmXYcjyy%SN?A+A4b zA3e!+ibYOFk>$2scsl6mbnHdgNdbKFCi(A_%_< z9{b1vTLlCN9Wk1(EmmD?`Uv~Xy6-wgtgoq;nhWe4H_+DBPWjA%*YDvLS!RCBL8*_0 zor^lUFij%fi8oJ-){7C-nN2bwb+G9ZOJe9|YktEL+nL@Uz*`pTMhph5{m_lePmV|2 z-+%5@{eOqLa+$1!+>zGANt+2^WoumK&C;f5&sjsaOP1!jdh6=GvC^^X>2)s|3trjJpj|03_ z^R?gu*+$FhXU3G}zn6T=VIuWLId%7<8irLwTAxn>)IEDfT~Zgu9<;wc!#hWbt>--6 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zLXWWDT>cNlSL*^@9}h69FeN-Nmw$r5S_-~-nUjXqC8_|2anqj&lBy9?J22M zx8(g9-+kaDui;=ie=s7FFqGg_6Q^xCm*kWvG-}}mFWuK<9jFZ%wD>MXK?ZFCzeoEZ zYNmnTqe~Dq%fNr7C)M#k|57T}6f6{xKXk6?v@97nM0MhiE1J=aBW8ai1#z*8dasM| g@!SEpI@?5;L2r=y6jY(KUbn+f#Gv-0X7=&@H~z%iR{#J2 diff --git a/project.yaml b/project.yaml index 1166ff41..b55de25e 100644 --- a/project.yaml +++ b/project.yaml @@ -55,6 +55,18 @@ actions: highly_sensitive: cohort: output/input_prevax.csv.gz + ## Implement study_definition for prevax_extf + + generate_study_population_prevax_extf: + run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_extf + --output-format csv.gz + needs: + - vax_eligibility_inputs + - generate_index_dates + outputs: + highly_sensitive: + cohort: output/input_prevax_extf.csv.gz + ## Implement study_definition for vax generate_study_population_vax: @@ -82,7 +94,7 @@ actions: ## Preprocess data - prevax preprocess_data_prevax: - run: r:latest analysis/preprocess/preprocess_data.R prevax + run: r:latest analysis/preprocess_data.R prevax needs: - generate_index_dates - generate_study_population_prevax @@ -91,13 +103,28 @@ actions: describe: output/describe_input_prevax_stage0.txt describe_venn: output/describe_venn_prevax.txt highly_sensitive: - cohort: output/input_prevax.rds.gz - venn: output/venn_prevax.rds.gz + cohort: output/input_prevax.rds + venn: output/venn_prevax.rds + + ## Preprocess data - prevax_extf + + preprocess_data_prevax_extf: + run: r:latest analysis/preprocess_data.R prevax_extf + needs: + - generate_index_dates + - generate_study_population_prevax_extf + outputs: + moderately_sensitive: + describe: output/describe_input_prevax_extf_stage0.txt + describe_venn: output/describe_venn_prevax_extf.txt + highly_sensitive: + cohort: output/input_prevax_extf.rds + venn: output/venn_prevax_extf.rds ## Preprocess data - vax preprocess_data_vax: - run: r:latest analysis/preprocess/preprocess_data.R vax + run: r:latest analysis/preprocess_data.R vax needs: - generate_index_dates - generate_study_population_vax @@ -112,7 +139,7 @@ actions: ## Preprocess data - unvax preprocess_data_unvax: - run: r:latest analysis/preprocess/preprocess_data.R unvax + run: r:latest analysis/preprocess_data.R unvax needs: - generate_index_dates - generate_study_population_unvax @@ -124,20 +151,21 @@ actions: cohort: output/input_unvax.rds venn: output/venn_unvax.rds - ## Stage 1 - Data cleaning - all cohorts + ## Data cleaning - all cohorts stage1_data_cleaning_all: - run: r:latest analysis/preprocess/Stage1_data_cleaning.R all + run: r:latest analysis/stage1_data_cleaning.R all needs: - preprocess_data_prevax + - preprocess_data_prevax_extf - preprocess_data_vax - preprocess_data_unvax - vax_eligibility_inputs outputs: moderately_sensitive: refactoring: output/meta_data_factors_*.csv - QA_rules: output/descriptives/QA_summary_*.csv - IE_criteria: output/descriptives/Cohort_flow_*.csv + QA_rules: output/QA_summary_*.csv + IE_criteria: output/Cohort_flow_*.csv histograms: output/numeric_histograms_*.svg highly_sensitive: cohort: output/input_*.rds @@ -150,6 +178,14 @@ actions: moderately_sensitive: describe_model_input: output/describe-input_prevax_stage1.txt + describe_file-input_prevax_extf_stage1: + run: r:latest analysis/describe_file.R input_prevax_extf_stage1 rds + needs: + - stage1_data_cleaning_all + outputs: + moderately_sensitive: + describe_model_input: output/describe-input_prevax_extf_stage1.txt + describe_file-input_vax_stage1: run: r:latest analysis/describe_file.R input_vax_stage1 rds needs: @@ -169,7 +205,7 @@ actions: ## Stage 5 - Run models make_model_input-cohort_prevax-main-addiction: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-addiction + run: r:latest analysis/make_model_input.R cohort_prevax-main-addiction needs: - stage1_data_cleaning_all outputs: @@ -179,7 +215,7 @@ actions: cox_ipw-cohort_prevax-main-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-addiction.csv @@ -189,29 +225,8 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-main-addiction.csv - make_model_input-cohort_prevax-main-addiction_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-addiction_extf - needs: - - stage1_data_cleaning_all - outputs: - highly_sensitive: - model_input: output/model_input-cohort_prevax-main-addiction_extf.rds - - cox_ipw-cohort_prevax-main-addiction_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-addiction_extf.rds - --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-addiction_extf.csv - needs: - - make_model_input-cohort_prevax-main-addiction_extf - outputs: - moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-addiction_extf.csv - make_model_input-cohort_prevax-main-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-main-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -221,7 +236,7 @@ actions: cox_ipw-cohort_prevax-main-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-anxiety_general.csv @@ -231,281 +246,302 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-main-anxiety_general.csv - make_model_input-cohort_prevax-main-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-anxiety_general_extf + make_model_input-cohort_prevax-main-anxiety_ptsd: + run: r:latest analysis/make_model_input.R cohort_prevax-main-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-main-anxiety_ptsd.rds - cox_ipw-cohort_prevax-main-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-anxiety_general_extf.rds + cox_ipw-cohort_prevax-main-anxiety_ptsd: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-anxiety_ptsd.csv needs: - - make_model_input-cohort_prevax-main-anxiety_general_extf + - make_model_input-cohort_prevax-main-anxiety_ptsd outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-main-anxiety_ptsd.csv - make_model_input-cohort_prevax-main-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-anxiety_ptsd + make_model_input-cohort_prevax-main-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-main-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-anxiety_ptsd.rds + model_input: output/model_input-cohort_prevax-main-depression.rds - cox_ipw-cohort_prevax-main-anxiety_ptsd: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-anxiety_ptsd.rds + cox_ipw-cohort_prevax-main-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-anxiety_ptsd.csv + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-depression.csv needs: - - make_model_input-cohort_prevax-main-anxiety_ptsd + - make_model_input-cohort_prevax-main-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-anxiety_ptsd.csv + model_output: output/model_output-cohort_prevax-main-depression.csv - make_model_input-cohort_prevax-main-anxiety_ptsd_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-anxiety_ptsd_extf + make_model_input-cohort_prevax-main-eating_disorders: + run: r:latest analysis/make_model_input.R cohort_prevax-main-eating_disorders needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-anxiety_ptsd_extf.rds + model_input: output/model_input-cohort_prevax-main-eating_disorders.rds - cox_ipw-cohort_prevax-main-anxiety_ptsd_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-anxiety_ptsd_extf.rds + cox_ipw-cohort_prevax-main-eating_disorders: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-anxiety_ptsd_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-eating_disorders.csv needs: - - make_model_input-cohort_prevax-main-anxiety_ptsd_extf + - make_model_input-cohort_prevax-main-eating_disorders outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-anxiety_ptsd_extf.csv + model_output: output/model_output-cohort_prevax-main-eating_disorders.csv - make_model_input-cohort_prevax-main-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-depression + make_model_input-cohort_prevax-main-self_harm: + run: r:latest analysis/make_model_input.R cohort_prevax-main-self_harm needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-depression.rds + model_input: output/model_input-cohort_prevax-main-self_harm.rds - cox_ipw-cohort_prevax-main-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-depression.rds - --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + cox_ipw-cohort_prevax-main-self_harm: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-self_harm.rds --ipw=TRUE + --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-depression.csv + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-self_harm.csv needs: - - make_model_input-cohort_prevax-main-depression + - make_model_input-cohort_prevax-main-self_harm outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-depression.csv + model_output: output/model_output-cohort_prevax-main-self_harm.csv - make_model_input-cohort_prevax-main-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-depression_extf + make_model_input-cohort_prevax-main-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-main-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-depression_extf.rds + model_input: output/model_input-cohort_prevax-main-serious_mental_illness.rds - cox_ipw-cohort_prevax-main-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-depression_extf.rds + cox_ipw-cohort_prevax-main-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-depression_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-main-depression_extf + - make_model_input-cohort_prevax-main-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-depression_extf.csv + model_output: output/model_output-cohort_prevax-main-serious_mental_illness.csv - make_model_input-cohort_prevax-main-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-eating_disorders + make_model_input-cohort_prevax-main-suicide: + run: r:latest analysis/make_model_input.R cohort_prevax-main-suicide needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-eating_disorders.rds + model_input: output/model_input-cohort_prevax-main-suicide.rds - cox_ipw-cohort_prevax-main-eating_disorders: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-eating_disorders.rds - --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + cox_ipw-cohort_prevax-main-suicide: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-suicide.rds --ipw=TRUE + --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-eating_disorders.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-suicide.csv needs: - - make_model_input-cohort_prevax-main-eating_disorders + - make_model_input-cohort_prevax-main-suicide outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-eating_disorders.csv + model_output: output/model_output-cohort_prevax-main-suicide.csv - make_model_input-cohort_prevax-main-eating_disorders_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-eating_disorders_extf + make_model_input-cohort_prevax_extf-main-addiction: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-addiction needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-eating_disorders_extf.rds + model_input: output/model_input-cohort_prevax_extf-main-addiction.rds - cox_ipw-cohort_prevax-main-eating_disorders_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-eating_disorders_extf.rds + cox_ipw-cohort_prevax_extf-main-addiction: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-main-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-eating_disorders_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-addiction.csv needs: - - make_model_input-cohort_prevax-main-eating_disorders_extf + - make_model_input-cohort_prevax_extf-main-addiction outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-eating_disorders_extf.csv + model_output: output/model_output-cohort_prevax_extf-main-addiction.csv - make_model_input-cohort_prevax-main-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-self_harm + make_model_input-cohort_prevax_extf-main-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-self_harm.rds + model_input: output/model_input-cohort_prevax_extf-main-anxiety_general.rds - cox_ipw-cohort_prevax-main-self_harm: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-self_harm.rds --ipw=TRUE - --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-self_harm.csv + cox_ipw-cohort_prevax_extf-main-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-main-anxiety_general.rds + --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-anxiety_general.csv needs: - - make_model_input-cohort_prevax-main-self_harm + - make_model_input-cohort_prevax_extf-main-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-self_harm.csv + model_output: output/model_output-cohort_prevax_extf-main-anxiety_general.csv - make_model_input-cohort_prevax-main-self_harm_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-self_harm_extf + make_model_input-cohort_prevax_extf-main-anxiety_ptsd: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-self_harm_extf.rds + model_input: output/model_input-cohort_prevax_extf-main-anxiety_ptsd.rds - cox_ipw-cohort_prevax-main-self_harm_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-self_harm_extf.rds + cox_ipw-cohort_prevax_extf-main-anxiety_ptsd: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-main-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-self_harm_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-anxiety_ptsd.csv needs: - - make_model_input-cohort_prevax-main-self_harm_extf + - make_model_input-cohort_prevax_extf-main-anxiety_ptsd outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-self_harm_extf.csv + model_output: output/model_output-cohort_prevax_extf-main-anxiety_ptsd.csv - make_model_input-cohort_prevax-main-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-serious_mental_illness + make_model_input-cohort_prevax_extf-main-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-main-depression.rds - cox_ipw-cohort_prevax-main-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-main-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-main-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-depression.csv needs: - - make_model_input-cohort_prevax-main-serious_mental_illness + - make_model_input-cohort_prevax_extf-main-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-main-depression.csv - make_model_input-cohort_prevax-main-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-main-eating_disorders: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-eating_disorders needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-main-eating_disorders.rds - cox_ipw-cohort_prevax-main-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-main-eating_disorders: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-main-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-serious_mental_illness_extf.csv + --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-eating_disorders.csv needs: - - make_model_input-cohort_prevax-main-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-main-eating_disorders outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-main-eating_disorders.csv - make_model_input-cohort_prevax-main-suicide: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-suicide + make_model_input-cohort_prevax_extf-main-self_harm: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-self_harm needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-suicide.rds + model_input: output/model_input-cohort_prevax_extf-main-self_harm.rds - cox_ipw-cohort_prevax-main-suicide: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-suicide.rds --ipw=TRUE - --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-suicide.csv + cox_ipw-cohort_prevax_extf-main-self_harm: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-main-self_harm.rds + --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-self_harm.csv needs: - - make_model_input-cohort_prevax-main-suicide + - make_model_input-cohort_prevax_extf-main-self_harm outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-suicide.csv + model_output: output/model_output-cohort_prevax_extf-main-self_harm.csv + + make_model_input-cohort_prevax_extf-main-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-serious_mental_illness + needs: + - stage1_data_cleaning_all + outputs: + highly_sensitive: + model_input: output/model_input-cohort_prevax_extf-main-serious_mental_illness.rds + + cox_ipw-cohort_prevax_extf-main-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-main-serious_mental_illness.rds + --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-serious_mental_illness.csv + needs: + - make_model_input-cohort_prevax_extf-main-serious_mental_illness + outputs: + moderately_sensitive: + model_output: output/model_output-cohort_prevax_extf-main-serious_mental_illness.csv - make_model_input-cohort_prevax-main-suicide_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-main-suicide_extf + make_model_input-cohort_prevax_extf-main-suicide: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-suicide needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-main-suicide_extf.rds + model_input: output/model_input-cohort_prevax_extf-main-suicide.rds - cox_ipw-cohort_prevax-main-suicide_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-suicide_extf.rds + cox_ipw-cohort_prevax_extf-main-suicide: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-main-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-suicide_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-suicide.csv needs: - - make_model_input-cohort_prevax-main-suicide_extf + - make_model_input-cohort_prevax_extf-main-suicide outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-suicide_extf.csv + model_output: output/model_output-cohort_prevax_extf-main-suicide.csv make_model_input-cohort_unvax-main-addiction: - run: r:latest analysis/model/make_model_input.R cohort_unvax-main-addiction + run: r:latest analysis/make_model_input.R cohort_unvax-main-addiction needs: - stage1_data_cleaning_all outputs: @@ -515,7 +551,7 @@ actions: cox_ipw-cohort_unvax-main-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-addiction.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-addiction.csv @@ -526,7 +562,7 @@ actions: model_output: output/model_output-cohort_unvax-main-addiction.csv make_model_input-cohort_unvax-main-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-main-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-main-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -536,7 +572,7 @@ actions: cox_ipw-cohort_unvax-main-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-anxiety_general.csv @@ -547,7 +583,7 @@ actions: model_output: output/model_output-cohort_unvax-main-anxiety_general.csv make_model_input-cohort_unvax-main-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_unvax-main-anxiety_ptsd + run: r:latest analysis/make_model_input.R cohort_unvax-main-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: @@ -557,7 +593,7 @@ actions: cox_ipw-cohort_unvax-main-anxiety_ptsd: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-anxiety_ptsd.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-anxiety_ptsd.csv @@ -568,7 +604,7 @@ actions: model_output: output/model_output-cohort_unvax-main-anxiety_ptsd.csv make_model_input-cohort_unvax-main-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-main-depression + run: r:latest analysis/make_model_input.R cohort_unvax-main-depression needs: - stage1_data_cleaning_all outputs: @@ -578,7 +614,7 @@ actions: cox_ipw-cohort_unvax-main-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-depression.csv @@ -589,7 +625,7 @@ actions: model_output: output/model_output-cohort_unvax-main-depression.csv make_model_input-cohort_unvax-main-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_unvax-main-eating_disorders + run: r:latest analysis/make_model_input.R cohort_unvax-main-eating_disorders needs: - stage1_data_cleaning_all outputs: @@ -599,7 +635,7 @@ actions: cox_ipw-cohort_unvax-main-eating_disorders: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-eating_disorders.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-eating_disorders.csv @@ -610,7 +646,7 @@ actions: model_output: output/model_output-cohort_unvax-main-eating_disorders.csv make_model_input-cohort_unvax-main-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_unvax-main-self_harm + run: r:latest analysis/make_model_input.R cohort_unvax-main-self_harm needs: - stage1_data_cleaning_all outputs: @@ -620,7 +656,7 @@ actions: cox_ipw-cohort_unvax-main-self_harm: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-self_harm.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-self_harm.csv @@ -631,7 +667,7 @@ actions: model_output: output/model_output-cohort_unvax-main-self_harm.csv make_model_input-cohort_unvax-main-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-main-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-main-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -641,7 +677,7 @@ actions: cox_ipw-cohort_unvax-main-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-serious_mental_illness.csv @@ -652,7 +688,7 @@ actions: model_output: output/model_output-cohort_unvax-main-serious_mental_illness.csv make_model_input-cohort_unvax-main-suicide: - run: r:latest analysis/model/make_model_input.R cohort_unvax-main-suicide + run: r:latest analysis/make_model_input.R cohort_unvax-main-suicide needs: - stage1_data_cleaning_all outputs: @@ -662,7 +698,7 @@ actions: cox_ipw-cohort_unvax-main-suicide: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-suicide.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-suicide.csv @@ -673,7 +709,7 @@ actions: model_output: output/model_output-cohort_unvax-main-suicide.csv make_model_input-cohort_vax-main-addiction: - run: r:latest analysis/model/make_model_input.R cohort_vax-main-addiction + run: r:latest analysis/make_model_input.R cohort_vax-main-addiction needs: - stage1_data_cleaning_all outputs: @@ -683,7 +719,7 @@ actions: cox_ipw-cohort_vax-main-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-addiction.csv @@ -694,7 +730,7 @@ actions: model_output: output/model_output-cohort_vax-main-addiction.csv make_model_input-cohort_vax-main-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-main-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-main-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -704,7 +740,7 @@ actions: cox_ipw-cohort_vax-main-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-anxiety_general.csv @@ -715,7 +751,7 @@ actions: model_output: output/model_output-cohort_vax-main-anxiety_general.csv make_model_input-cohort_vax-main-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_vax-main-anxiety_ptsd + run: r:latest analysis/make_model_input.R cohort_vax-main-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: @@ -725,7 +761,7 @@ actions: cox_ipw-cohort_vax-main-anxiety_ptsd: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-anxiety_ptsd.csv @@ -736,7 +772,7 @@ actions: model_output: output/model_output-cohort_vax-main-anxiety_ptsd.csv make_model_input-cohort_vax-main-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-main-depression + run: r:latest analysis/make_model_input.R cohort_vax-main-depression needs: - stage1_data_cleaning_all outputs: @@ -746,7 +782,7 @@ actions: cox_ipw-cohort_vax-main-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-depression.csv @@ -757,7 +793,7 @@ actions: model_output: output/model_output-cohort_vax-main-depression.csv make_model_input-cohort_vax-main-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_vax-main-eating_disorders + run: r:latest analysis/make_model_input.R cohort_vax-main-eating_disorders needs: - stage1_data_cleaning_all outputs: @@ -767,7 +803,7 @@ actions: cox_ipw-cohort_vax-main-eating_disorders: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-eating_disorders.csv @@ -778,7 +814,7 @@ actions: model_output: output/model_output-cohort_vax-main-eating_disorders.csv make_model_input-cohort_vax-main-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_vax-main-self_harm + run: r:latest analysis/make_model_input.R cohort_vax-main-self_harm needs: - stage1_data_cleaning_all outputs: @@ -788,7 +824,7 @@ actions: cox_ipw-cohort_vax-main-self_harm: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-self_harm.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-self_harm.csv @@ -799,7 +835,7 @@ actions: model_output: output/model_output-cohort_vax-main-self_harm.csv make_model_input-cohort_vax-main-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-main-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-main-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -809,7 +845,7 @@ actions: cox_ipw-cohort_vax-main-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-serious_mental_illness.csv @@ -820,7 +856,7 @@ actions: model_output: output/model_output-cohort_vax-main-serious_mental_illness.csv make_model_input-cohort_vax-main-suicide: - run: r:latest analysis/model/make_model_input.R cohort_vax-main-suicide + run: r:latest analysis/make_model_input.R cohort_vax-main-suicide needs: - stage1_data_cleaning_all outputs: @@ -830,7 +866,7 @@ actions: cox_ipw-cohort_vax-main-suicide: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-suicide.csv @@ -841,7 +877,7 @@ actions: model_output: output/model_output-cohort_vax-main-suicide.csv make_model_input-cohort_prevax-sub_age_18_39-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_18_39-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -851,7 +887,7 @@ actions: cox_ipw-cohort_prevax-sub_age_18_39-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-anxiety_general.csv @@ -861,113 +897,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_age_18_39-anxiety_general.csv - make_model_input-cohort_prevax-sub_age_18_39-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-anxiety_general_extf + make_model_input-cohort_prevax-sub_age_18_39-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_18_39-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_18_39-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_age_18_39-depression.rds - cox_ipw-cohort_prevax-sub_age_18_39-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_age_18_39-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-depression.csv needs: - - make_model_input-cohort_prevax-sub_age_18_39-anxiety_general_extf + - make_model_input-cohort_prevax-sub_age_18_39-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_18_39-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_age_18_39-depression.csv - make_model_input-cohort_prevax-sub_age_18_39-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-depression + make_model_input-cohort_prevax-sub_age_18_39-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_18_39-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_18_39-depression.rds + model_input: output/model_input-cohort_prevax-sub_age_18_39-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_age_18_39-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-depression.rds + cox_ipw-cohort_prevax-sub_age_18_39-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-depression.csv + --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_age_18_39-depression + - make_model_input-cohort_prevax-sub_age_18_39-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_18_39-depression.csv + model_output: output/model_output-cohort_prevax-sub_age_18_39-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_age_18_39-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-depression_extf + make_model_input-cohort_prevax_extf-sub_age_18_39-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_18_39-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_18_39-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_18_39-anxiety_general.rds - cox_ipw-cohort_prevax-sub_age_18_39-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_age_18_39-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_18_39-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_18_39-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_age_18_39-depression_extf + - make_model_input-cohort_prevax_extf-sub_age_18_39-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_18_39-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_18_39-anxiety_general.csv - make_model_input-cohort_prevax-sub_age_18_39-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_age_18_39-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_18_39-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_18_39-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_18_39-depression.rds - cox_ipw-cohort_prevax-sub_age_18_39-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_age_18_39-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_18_39-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_18_39-depression.csv needs: - - make_model_input-cohort_prevax-sub_age_18_39-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_age_18_39-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_18_39-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_18_39-depression.csv - make_model_input-cohort_prevax-sub_age_18_39-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_18_39-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_18_39-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_age_18_39-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_age_18_39-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_age_18_39-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_18_39-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.csv make_model_input-cohort_unvax-sub_age_18_39-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_18_39-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -977,7 +1013,7 @@ actions: cox_ipw-cohort_unvax-sub_age_18_39-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-anxiety_general.csv @@ -988,7 +1024,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_18_39-anxiety_general.csv make_model_input-cohort_unvax-sub_age_18_39-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_18_39-depression needs: - stage1_data_cleaning_all outputs: @@ -998,7 +1034,7 @@ actions: cox_ipw-cohort_unvax-sub_age_18_39-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-depression.csv @@ -1009,7 +1045,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_18_39-depression.csv make_model_input-cohort_unvax-sub_age_18_39-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_18_39-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1019,7 +1055,7 @@ actions: cox_ipw-cohort_unvax-sub_age_18_39-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-serious_mental_illness.csv @@ -1030,7 +1066,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_18_39-serious_mental_illness.csv make_model_input-cohort_vax-sub_age_18_39-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1040,7 +1076,7 @@ actions: cox_ipw-cohort_vax-sub_age_18_39-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-anxiety_general.csv @@ -1051,7 +1087,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_18_39-anxiety_general.csv make_model_input-cohort_vax-sub_age_18_39-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-depression needs: - stage1_data_cleaning_all outputs: @@ -1061,7 +1097,7 @@ actions: cox_ipw-cohort_vax-sub_age_18_39-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-depression.csv @@ -1072,7 +1108,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_18_39-depression.csv make_model_input-cohort_vax-sub_age_18_39-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1082,7 +1118,7 @@ actions: cox_ipw-cohort_vax-sub_age_18_39-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-serious_mental_illness.csv @@ -1093,7 +1129,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_18_39-serious_mental_illness.csv make_model_input-cohort_prevax-sub_age_40_59-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_40_59-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1103,7 +1139,7 @@ actions: cox_ipw-cohort_prevax-sub_age_40_59-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-anxiety_general.csv @@ -1113,113 +1149,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_age_40_59-anxiety_general.csv - make_model_input-cohort_prevax-sub_age_40_59-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-anxiety_general_extf + make_model_input-cohort_prevax-sub_age_40_59-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_40_59-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_40_59-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_age_40_59-depression.rds - cox_ipw-cohort_prevax-sub_age_40_59-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_age_40_59-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-depression.csv needs: - - make_model_input-cohort_prevax-sub_age_40_59-anxiety_general_extf + - make_model_input-cohort_prevax-sub_age_40_59-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_40_59-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_age_40_59-depression.csv - make_model_input-cohort_prevax-sub_age_40_59-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-depression + make_model_input-cohort_prevax-sub_age_40_59-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_40_59-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_40_59-depression.rds + model_input: output/model_input-cohort_prevax-sub_age_40_59-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_age_40_59-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-depression.rds + cox_ipw-cohort_prevax-sub_age_40_59-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-depression.csv + --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_age_40_59-depression + - make_model_input-cohort_prevax-sub_age_40_59-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_40_59-depression.csv + model_output: output/model_output-cohort_prevax-sub_age_40_59-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_age_40_59-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-depression_extf + make_model_input-cohort_prevax_extf-sub_age_40_59-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_40_59-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_40_59-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_40_59-anxiety_general.rds - cox_ipw-cohort_prevax-sub_age_40_59-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_age_40_59-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_40_59-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_40_59-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_age_40_59-depression_extf + - make_model_input-cohort_prevax_extf-sub_age_40_59-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_40_59-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_40_59-anxiety_general.csv - make_model_input-cohort_prevax-sub_age_40_59-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_age_40_59-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_40_59-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_40_59-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_40_59-depression.rds - cox_ipw-cohort_prevax-sub_age_40_59-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_age_40_59-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_40_59-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_40_59-depression.csv needs: - - make_model_input-cohort_prevax-sub_age_40_59-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_age_40_59-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_40_59-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_40_59-depression.csv - make_model_input-cohort_prevax-sub_age_40_59-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_40_59-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_40_59-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_age_40_59-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_age_40_59-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_age_40_59-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_40_59-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.csv make_model_input-cohort_unvax-sub_age_40_59-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_40_59-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1229,7 +1265,7 @@ actions: cox_ipw-cohort_unvax-sub_age_40_59-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-anxiety_general.csv @@ -1240,7 +1276,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_40_59-anxiety_general.csv make_model_input-cohort_unvax-sub_age_40_59-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_40_59-depression needs: - stage1_data_cleaning_all outputs: @@ -1250,7 +1286,7 @@ actions: cox_ipw-cohort_unvax-sub_age_40_59-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-depression.csv @@ -1261,7 +1297,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_40_59-depression.csv make_model_input-cohort_unvax-sub_age_40_59-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_40_59-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1271,7 +1307,7 @@ actions: cox_ipw-cohort_unvax-sub_age_40_59-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-serious_mental_illness.csv @@ -1282,7 +1318,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_40_59-serious_mental_illness.csv make_model_input-cohort_vax-sub_age_40_59-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_40_59-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1292,7 +1328,7 @@ actions: cox_ipw-cohort_vax-sub_age_40_59-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-anxiety_general.csv @@ -1303,7 +1339,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_40_59-anxiety_general.csv make_model_input-cohort_vax-sub_age_40_59-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_40_59-depression needs: - stage1_data_cleaning_all outputs: @@ -1313,7 +1349,7 @@ actions: cox_ipw-cohort_vax-sub_age_40_59-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-depression.csv @@ -1324,7 +1360,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_40_59-depression.csv make_model_input-cohort_vax-sub_age_40_59-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_40_59-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1334,7 +1370,7 @@ actions: cox_ipw-cohort_vax-sub_age_40_59-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-serious_mental_illness.csv @@ -1345,7 +1381,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_40_59-serious_mental_illness.csv make_model_input-cohort_prevax-sub_age_60_79-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_60_79-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1355,7 +1391,7 @@ actions: cox_ipw-cohort_prevax-sub_age_60_79-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-anxiety_general.csv @@ -1365,113 +1401,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_age_60_79-anxiety_general.csv - make_model_input-cohort_prevax-sub_age_60_79-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-anxiety_general_extf + make_model_input-cohort_prevax-sub_age_60_79-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_60_79-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_60_79-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_age_60_79-depression.rds - cox_ipw-cohort_prevax-sub_age_60_79-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_age_60_79-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-depression.csv needs: - - make_model_input-cohort_prevax-sub_age_60_79-anxiety_general_extf + - make_model_input-cohort_prevax-sub_age_60_79-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_60_79-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_age_60_79-depression.csv - make_model_input-cohort_prevax-sub_age_60_79-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-depression + make_model_input-cohort_prevax-sub_age_60_79-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_60_79-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_60_79-depression.rds + model_input: output/model_input-cohort_prevax-sub_age_60_79-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_age_60_79-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-depression.rds + cox_ipw-cohort_prevax-sub_age_60_79-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-depression.csv + --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_age_60_79-depression + - make_model_input-cohort_prevax-sub_age_60_79-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_60_79-depression.csv + model_output: output/model_output-cohort_prevax-sub_age_60_79-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_age_60_79-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-depression_extf + make_model_input-cohort_prevax_extf-sub_age_60_79-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_60_79-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_60_79-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_60_79-anxiety_general.rds - cox_ipw-cohort_prevax-sub_age_60_79-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_age_60_79-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_60_79-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_60_79-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_age_60_79-depression_extf + - make_model_input-cohort_prevax_extf-sub_age_60_79-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_60_79-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_60_79-anxiety_general.csv - make_model_input-cohort_prevax-sub_age_60_79-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_age_60_79-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_60_79-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_60_79-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_60_79-depression.rds - cox_ipw-cohort_prevax-sub_age_60_79-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_age_60_79-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_60_79-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_60_79-depression.csv needs: - - make_model_input-cohort_prevax-sub_age_60_79-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_age_60_79-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_60_79-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_60_79-depression.csv - make_model_input-cohort_prevax-sub_age_60_79-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_age_60_79-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_60_79-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_60_79-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_60_79-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_age_60_79-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_age_60_79-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_60_79-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_60_79-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_age_60_79-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_age_60_79-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_60_79-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_60_79-serious_mental_illness.csv make_model_input-cohort_unvax-sub_age_60_79-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_60_79-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1481,7 +1517,7 @@ actions: cox_ipw-cohort_unvax-sub_age_60_79-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-anxiety_general.csv @@ -1492,7 +1528,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_60_79-anxiety_general.csv make_model_input-cohort_unvax-sub_age_60_79-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_60_79-depression needs: - stage1_data_cleaning_all outputs: @@ -1502,7 +1538,7 @@ actions: cox_ipw-cohort_unvax-sub_age_60_79-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-depression.csv @@ -1513,7 +1549,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_60_79-depression.csv make_model_input-cohort_unvax-sub_age_60_79-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_60_79-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1523,7 +1559,7 @@ actions: cox_ipw-cohort_unvax-sub_age_60_79-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-serious_mental_illness.csv @@ -1534,7 +1570,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_60_79-serious_mental_illness.csv make_model_input-cohort_vax-sub_age_60_79-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_60_79-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1544,7 +1580,7 @@ actions: cox_ipw-cohort_vax-sub_age_60_79-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-anxiety_general.csv @@ -1555,7 +1591,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_60_79-anxiety_general.csv make_model_input-cohort_vax-sub_age_60_79-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_60_79-depression needs: - stage1_data_cleaning_all outputs: @@ -1565,7 +1601,7 @@ actions: cox_ipw-cohort_vax-sub_age_60_79-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-depression.csv @@ -1576,7 +1612,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_60_79-depression.csv make_model_input-cohort_vax-sub_age_60_79-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_60_79-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1586,7 +1622,7 @@ actions: cox_ipw-cohort_vax-sub_age_60_79-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-serious_mental_illness.csv @@ -1597,7 +1633,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_60_79-serious_mental_illness.csv make_model_input-cohort_prevax-sub_age_80_110-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_80_110-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1607,7 +1643,7 @@ actions: cox_ipw-cohort_prevax-sub_age_80_110-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-anxiety_general.csv @@ -1617,113 +1653,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_age_80_110-anxiety_general.csv - make_model_input-cohort_prevax-sub_age_80_110-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-anxiety_general_extf + make_model_input-cohort_prevax-sub_age_80_110-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_80_110-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_80_110-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_age_80_110-depression.rds - cox_ipw-cohort_prevax-sub_age_80_110-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_age_80_110-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-depression.csv needs: - - make_model_input-cohort_prevax-sub_age_80_110-anxiety_general_extf + - make_model_input-cohort_prevax-sub_age_80_110-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_80_110-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_age_80_110-depression.csv - make_model_input-cohort_prevax-sub_age_80_110-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-depression + make_model_input-cohort_prevax-sub_age_80_110-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_age_80_110-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_80_110-depression.rds + model_input: output/model_input-cohort_prevax-sub_age_80_110-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_age_80_110-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-depression.rds + cox_ipw-cohort_prevax-sub_age_80_110-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-depression.csv + --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_age_80_110-depression + - make_model_input-cohort_prevax-sub_age_80_110-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_80_110-depression.csv + model_output: output/model_output-cohort_prevax-sub_age_80_110-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_age_80_110-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-depression_extf + make_model_input-cohort_prevax_extf-sub_age_80_110-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_80_110-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_80_110-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_80_110-anxiety_general.rds - cox_ipw-cohort_prevax-sub_age_80_110-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_age_80_110-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_80_110-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_80_110-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_age_80_110-depression_extf + - make_model_input-cohort_prevax_extf-sub_age_80_110-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_80_110-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_80_110-anxiety_general.csv - make_model_input-cohort_prevax-sub_age_80_110-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_age_80_110-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_80_110-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_80_110-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_80_110-depression.rds - cox_ipw-cohort_prevax-sub_age_80_110-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_age_80_110-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_80_110-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_80_110-depression.csv needs: - - make_model_input-cohort_prevax-sub_age_80_110-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_age_80_110-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_80_110-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_80_110-depression.csv - make_model_input-cohort_prevax-sub_age_80_110-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_age_80_110-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_80_110-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_age_80_110-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_age_80_110-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_age_80_110-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_age_80_110-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_age_80_110-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_80_110-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_age_80_110-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_age_80_110-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_age_80_110-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_age_80_110-serious_mental_illness.csv make_model_input-cohort_unvax-sub_age_80_110-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_80_110-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1733,7 +1769,7 @@ actions: cox_ipw-cohort_unvax-sub_age_80_110-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-anxiety_general.csv @@ -1744,7 +1780,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_80_110-anxiety_general.csv make_model_input-cohort_unvax-sub_age_80_110-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_80_110-depression needs: - stage1_data_cleaning_all outputs: @@ -1754,7 +1790,7 @@ actions: cox_ipw-cohort_unvax-sub_age_80_110-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-depression.csv @@ -1765,7 +1801,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_80_110-depression.csv make_model_input-cohort_unvax-sub_age_80_110-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_80_110-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1775,7 +1811,7 @@ actions: cox_ipw-cohort_unvax-sub_age_80_110-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-serious_mental_illness.csv @@ -1786,7 +1822,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_age_80_110-serious_mental_illness.csv make_model_input-cohort_vax-sub_age_80_110-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_80_110-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1796,7 +1832,7 @@ actions: cox_ipw-cohort_vax-sub_age_80_110-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-anxiety_general.csv @@ -1807,7 +1843,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_80_110-anxiety_general.csv make_model_input-cohort_vax-sub_age_80_110-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_80_110-depression needs: - stage1_data_cleaning_all outputs: @@ -1817,7 +1853,7 @@ actions: cox_ipw-cohort_vax-sub_age_80_110-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-depression.csv @@ -1828,7 +1864,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_80_110-depression.csv make_model_input-cohort_vax-sub_age_80_110-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_age_80_110-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1838,7 +1874,7 @@ actions: cox_ipw-cohort_vax-sub_age_80_110-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-serious_mental_illness.csv @@ -1849,7 +1885,7 @@ actions: model_output: output/model_output-cohort_vax-sub_age_80_110-serious_mental_illness.csv make_model_input-cohort_unvax-sub_covid_history-addiction: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-addiction + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_history-addiction needs: - stage1_data_cleaning_all outputs: @@ -1859,7 +1895,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_history-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-addiction.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-addiction.csv @@ -1870,7 +1906,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_history-addiction.csv make_model_input-cohort_unvax-sub_covid_history-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_history-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -1880,7 +1916,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_history-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-anxiety_general.csv @@ -1891,7 +1927,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_history-anxiety_general.csv make_model_input-cohort_unvax-sub_covid_history-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-anxiety_ptsd + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_history-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: @@ -1901,7 +1937,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_history-anxiety_ptsd: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-anxiety_ptsd.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-anxiety_ptsd.csv @@ -1912,7 +1948,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_history-anxiety_ptsd.csv make_model_input-cohort_unvax-sub_covid_history-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_history-depression needs: - stage1_data_cleaning_all outputs: @@ -1922,7 +1958,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_history-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-depression.csv @@ -1933,7 +1969,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_history-depression.csv make_model_input-cohort_unvax-sub_covid_history-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-eating_disorders + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_history-eating_disorders needs: - stage1_data_cleaning_all outputs: @@ -1943,7 +1979,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_history-eating_disorders: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-eating_disorders.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-eating_disorders.csv @@ -1954,7 +1990,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_history-eating_disorders.csv make_model_input-cohort_unvax-sub_covid_history-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-self_harm + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_history-self_harm needs: - stage1_data_cleaning_all outputs: @@ -1964,7 +2000,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_history-self_harm: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-self_harm.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-self_harm.csv @@ -1975,7 +2011,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_history-self_harm.csv make_model_input-cohort_unvax-sub_covid_history-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_history-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -1985,7 +2021,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_history-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-serious_mental_illness.csv @@ -1996,7 +2032,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_history-serious_mental_illness.csv make_model_input-cohort_unvax-sub_covid_history-suicide: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-suicide + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_history-suicide needs: - stage1_data_cleaning_all outputs: @@ -2006,7 +2042,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_history-suicide: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-suicide.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-suicide.csv @@ -2017,7 +2053,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_history-suicide.csv make_model_input-cohort_vax-sub_covid_history-addiction: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-addiction + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-addiction needs: - stage1_data_cleaning_all outputs: @@ -2027,7 +2063,7 @@ actions: cox_ipw-cohort_vax-sub_covid_history-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-addiction.csv @@ -2038,7 +2074,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_history-addiction.csv make_model_input-cohort_vax-sub_covid_history-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -2048,7 +2084,7 @@ actions: cox_ipw-cohort_vax-sub_covid_history-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-anxiety_general.csv @@ -2059,7 +2095,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_history-anxiety_general.csv make_model_input-cohort_vax-sub_covid_history-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-anxiety_ptsd + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: @@ -2069,7 +2105,7 @@ actions: cox_ipw-cohort_vax-sub_covid_history-anxiety_ptsd: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-anxiety_ptsd.csv @@ -2080,7 +2116,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_history-anxiety_ptsd.csv make_model_input-cohort_vax-sub_covid_history-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-depression needs: - stage1_data_cleaning_all outputs: @@ -2090,7 +2126,7 @@ actions: cox_ipw-cohort_vax-sub_covid_history-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-depression.csv @@ -2101,7 +2137,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_history-depression.csv make_model_input-cohort_vax-sub_covid_history-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-eating_disorders + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-eating_disorders needs: - stage1_data_cleaning_all outputs: @@ -2111,7 +2147,7 @@ actions: cox_ipw-cohort_vax-sub_covid_history-eating_disorders: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-eating_disorders.csv @@ -2122,7 +2158,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_history-eating_disorders.csv make_model_input-cohort_vax-sub_covid_history-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-self_harm + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-self_harm needs: - stage1_data_cleaning_all outputs: @@ -2132,7 +2168,7 @@ actions: cox_ipw-cohort_vax-sub_covid_history-self_harm: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-self_harm.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-self_harm.csv @@ -2143,7 +2179,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_history-self_harm.csv make_model_input-cohort_vax-sub_covid_history-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -2153,7 +2189,7 @@ actions: cox_ipw-cohort_vax-sub_covid_history-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-serious_mental_illness.csv @@ -2164,7 +2200,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_history-serious_mental_illness.csv make_model_input-cohort_vax-sub_covid_history-suicide: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-suicide + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-suicide needs: - stage1_data_cleaning_all outputs: @@ -2174,7 +2210,7 @@ actions: cox_ipw-cohort_vax-sub_covid_history-suicide: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-suicide.csv @@ -2185,7 +2221,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_history-suicide.csv make_model_input-cohort_prevax-sub_covid_hospitalised-addiction: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-addiction + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_hospitalised-addiction needs: - stage1_data_cleaning_all outputs: @@ -2195,7 +2231,7 @@ actions: cox_ipw-cohort_prevax-sub_covid_hospitalised-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-addiction.csv @@ -2205,323 +2241,323 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-addiction.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-addiction_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-addiction_extf + make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_hospitalised-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-addiction_extf.rds + model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-addiction_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-addiction_extf.rds + cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-addiction_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-addiction_extf + - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-addiction_extf.csv + model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_general.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-anxiety_general + make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_hospitalised-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general.rds + model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general.rds + cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-anxiety_general.csv + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general + - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_general.csv + model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-anxiety_general_extf + make_model_input-cohort_prevax-sub_covid_hospitalised-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_hospitalised-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-depression.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_covid_hospitalised-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-depression.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general_extf + - make_model_input-cohort_prevax-sub_covid_hospitalised-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-depression.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-anxiety_ptsd + make_model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_hospitalised-eating_disorders needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.rds + model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.rds + cox_ipw-cohort_prevax-sub_covid_hospitalised-eating_disorders: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-eating_disorders.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd + - make_model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.csv + model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-eating_disorders.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-anxiety_ptsd_extf + make_model_input-cohort_prevax-sub_covid_hospitalised-self_harm: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_hospitalised-self_harm needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd_extf.rds + model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-self_harm.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd_extf.rds + cox_ipw-cohort_prevax-sub_covid_hospitalised-self_harm: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-self_harm.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-self_harm.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd_extf + - make_model_input-cohort_prevax-sub_covid_hospitalised-self_harm outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd_extf.csv + model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-self_harm.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-depression + make_model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_hospitalised-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-depression.rds + model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-depression.rds + cox_ipw-cohort_prevax-sub_covid_hospitalised-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-depression + - make_model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-depression.csv + model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-depression_extf + make_model_input-cohort_prevax-sub_covid_hospitalised-suicide: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_hospitalised-suicide needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-depression_extf.rds + model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-suicide.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-depression_extf.rds + cox_ipw-cohort_prevax-sub_covid_hospitalised-suicide: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-depression_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-suicide.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-depression_extf + - make_model_input-cohort_prevax-sub_covid_hospitalised-suicide outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-depression_extf.csv + model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-suicide.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-eating_disorders + make_model_input-cohort_prevax_extf-sub_covid_hospitalised-addiction: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-addiction needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-addiction.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-eating_disorders: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders.rds + cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-addiction: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_hospitalised-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-eating_disorders.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-addiction.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders + - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-addiction outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-eating_disorders.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-addiction.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-eating_disorders_extf + make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-eating_disorders_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders_extf.rds + cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-eating_disorders_extf.csv + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders_extf + - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-eating_disorders_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-self_harm + make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-self_harm.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-self_harm: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-self_harm.rds + cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-self_harm.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-self_harm + - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-self_harm.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-self_harm_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-self_harm_extf + make_model_input-cohort_prevax_extf-sub_covid_hospitalised-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-self_harm_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-depression.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-self_harm_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-self_harm_extf.rds + cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_hospitalised-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-self_harm_extf.csv + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-depression.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-self_harm_extf + - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-self_harm_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-depression.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-eating_disorders needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_covid_hospitalised-self_harm: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-self_harm needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-self_harm.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-self_harm: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_hospitalised-self_harm.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-serious_mental_illness_extf.csv + --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-self_harm.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-self_harm outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-self_harm.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-suicide: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-suicide + make_model_input-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-suicide.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-suicide: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-suicide.rds + cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-suicide.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-suicide + - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-suicide.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_covid_hospitalised-suicide_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-suicide_extf + make_model_input-cohort_prevax_extf-sub_covid_hospitalised-suicide: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-suicide needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-suicide_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-suicide.rds - cox_ipw-cohort_prevax-sub_covid_hospitalised-suicide_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-suicide_extf.rds + cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-suicide: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_hospitalised-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-suicide_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-suicide.csv needs: - - make_model_input-cohort_prevax-sub_covid_hospitalised-suicide_extf + - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-suicide outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-suicide_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-suicide.csv make_model_input-cohort_unvax-sub_covid_hospitalised-addiction: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-addiction + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-addiction needs: - stage1_data_cleaning_all outputs: @@ -2531,7 +2567,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_hospitalised-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-addiction.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-addiction.csv @@ -2542,7 +2578,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-addiction.csv make_model_input-cohort_unvax-sub_covid_hospitalised-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -2552,7 +2588,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-anxiety_general.csv @@ -2563,7 +2599,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-anxiety_general.csv make_model_input-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-anxiety_ptsd + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: @@ -2573,7 +2609,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd.csv @@ -2584,7 +2620,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd.csv make_model_input-cohort_unvax-sub_covid_hospitalised-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-depression needs: - stage1_data_cleaning_all outputs: @@ -2594,7 +2630,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_hospitalised-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-depression.csv @@ -2605,7 +2641,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-depression.csv make_model_input-cohort_unvax-sub_covid_hospitalised-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-eating_disorders + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-eating_disorders needs: - stage1_data_cleaning_all outputs: @@ -2615,7 +2651,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_hospitalised-eating_disorders: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-eating_disorders.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-eating_disorders.csv @@ -2626,7 +2662,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-eating_disorders.csv make_model_input-cohort_unvax-sub_covid_hospitalised-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-self_harm + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-self_harm needs: - stage1_data_cleaning_all outputs: @@ -2636,7 +2672,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_hospitalised-self_harm: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-self_harm.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-self_harm.csv @@ -2647,7 +2683,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-self_harm.csv make_model_input-cohort_unvax-sub_covid_hospitalised-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -2657,7 +2693,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_hospitalised-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-serious_mental_illness.csv @@ -2668,7 +2704,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-serious_mental_illness.csv make_model_input-cohort_unvax-sub_covid_hospitalised-suicide: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-suicide + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-suicide needs: - stage1_data_cleaning_all outputs: @@ -2678,7 +2714,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_hospitalised-suicide: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-suicide.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-suicide.csv @@ -2689,7 +2725,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-suicide.csv make_model_input-cohort_vax-sub_covid_hospitalised-addiction: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-addiction + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-addiction needs: - stage1_data_cleaning_all outputs: @@ -2699,7 +2735,7 @@ actions: cox_ipw-cohort_vax-sub_covid_hospitalised-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-addiction.csv @@ -2710,7 +2746,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_hospitalised-addiction.csv make_model_input-cohort_vax-sub_covid_hospitalised-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -2720,7 +2756,7 @@ actions: cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-anxiety_general.csv @@ -2731,7 +2767,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_hospitalised-anxiety_general.csv make_model_input-cohort_vax-sub_covid_hospitalised-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-anxiety_ptsd + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: @@ -2741,7 +2777,7 @@ actions: cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_ptsd: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-anxiety_ptsd.csv @@ -2752,7 +2788,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_hospitalised-anxiety_ptsd.csv make_model_input-cohort_vax-sub_covid_hospitalised-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-depression needs: - stage1_data_cleaning_all outputs: @@ -2762,7 +2798,7 @@ actions: cox_ipw-cohort_vax-sub_covid_hospitalised-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-depression.csv @@ -2773,7 +2809,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_hospitalised-depression.csv make_model_input-cohort_vax-sub_covid_hospitalised-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-eating_disorders + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-eating_disorders needs: - stage1_data_cleaning_all outputs: @@ -2783,7 +2819,7 @@ actions: cox_ipw-cohort_vax-sub_covid_hospitalised-eating_disorders: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-eating_disorders.csv @@ -2794,7 +2830,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_hospitalised-eating_disorders.csv make_model_input-cohort_vax-sub_covid_hospitalised-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-self_harm + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-self_harm needs: - stage1_data_cleaning_all outputs: @@ -2804,7 +2840,7 @@ actions: cox_ipw-cohort_vax-sub_covid_hospitalised-self_harm: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-self_harm.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-self_harm.csv @@ -2815,7 +2851,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_hospitalised-self_harm.csv make_model_input-cohort_vax-sub_covid_hospitalised-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -2825,7 +2861,7 @@ actions: cox_ipw-cohort_vax-sub_covid_hospitalised-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-serious_mental_illness.csv @@ -2836,7 +2872,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_hospitalised-serious_mental_illness.csv make_model_input-cohort_vax-sub_covid_hospitalised-suicide: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-suicide + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-suicide needs: - stage1_data_cleaning_all outputs: @@ -2846,7 +2882,7 @@ actions: cox_ipw-cohort_vax-sub_covid_hospitalised-suicide: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-suicide.csv @@ -2857,7 +2893,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_hospitalised-suicide.csv make_model_input-cohort_prevax-sub_covid_nonhospitalised-addiction: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-addiction + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-addiction needs: - stage1_data_cleaning_all outputs: @@ -2867,7 +2903,7 @@ actions: cox_ipw-cohort_prevax-sub_covid_nonhospitalised-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-addiction.csv @@ -2877,29 +2913,8 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-addiction.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-addiction_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-addiction_extf - needs: - - stage1_data_cleaning_all - outputs: - highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-addiction_extf.rds - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-addiction_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-addiction_extf.rds - --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-addiction_extf.csv - needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-addiction_extf - outputs: - moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-addiction_extf.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -2909,7 +2924,7 @@ actions: cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_general.csv @@ -2919,281 +2934,302 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_general.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-anxiety_general_extf + make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_general_extf + - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd + make_model_input-cohort_prevax-sub_covid_nonhospitalised-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.rds + model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-depression.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.rds + cox_ipw-cohort_prevax-sub_covid_nonhospitalised-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.csv + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-depression.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd + - make_model_input-cohort_prevax-sub_covid_nonhospitalised-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.csv + model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-depression.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd_extf + make_model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-eating_disorders needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd_extf.rds + model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd_extf.rds + cox_ipw-cohort_prevax-sub_covid_nonhospitalised-eating_disorders: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd_extf + - make_model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd_extf.csv + model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-depression + make_model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-self_harm needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-depression.rds + model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-depression.rds + cox_ipw-cohort_prevax-sub_covid_nonhospitalised-self_harm: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-depression.csv + --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-self_harm.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-depression + - make_model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-depression.csv + model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-self_harm.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-depression_extf + make_model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-depression_extf.rds + model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-depression_extf.rds + cox_ipw-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-depression_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-depression_extf + - make_model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-depression_extf.csv + model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-eating_disorders + make_model_input-cohort_prevax-sub_covid_nonhospitalised-suicide: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-suicide needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.rds + model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-suicide.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-eating_disorders: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.rds + cox_ipw-cohort_prevax-sub_covid_nonhospitalised-suicide: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-suicide.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders + - make_model_input-cohort_prevax-sub_covid_nonhospitalised-suicide outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.csv + model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-suicide.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-eating_disorders_extf + make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-addiction: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-addiction needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-addiction.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-eating_disorders_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders_extf.rds + cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-addiction: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_nonhospitalised-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-eating_disorders_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-addiction.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders_extf + - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-addiction outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-eating_disorders_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-addiction.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-self_harm + make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-self_harm: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm.rds + cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-self_harm.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm + - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-self_harm.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-self_harm_extf + make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-self_harm_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm_extf.rds + cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-self_harm_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm_extf + - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-self_harm_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-depression.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_nonhospitalised-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-depression.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-depression.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness_extf.csv + --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-suicide: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-suicide + make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-self_harm needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-suicide.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-suicide: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-suicide.rds + cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-suicide.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-suicide + - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-suicide.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm.csv + + make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness + needs: + - stage1_data_cleaning_all + outputs: + highly_sensitive: + model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness.rds + + cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness.rds + --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness.csv + needs: + - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness + outputs: + moderately_sensitive: + model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_covid_nonhospitalised-suicide_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-suicide_extf + make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-suicide: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-suicide needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-suicide_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-suicide.rds - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-suicide_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-suicide_extf.rds + cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-suicide: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_covid_nonhospitalised-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-suicide_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-suicide.csv needs: - - make_model_input-cohort_prevax-sub_covid_nonhospitalised-suicide_extf + - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-suicide outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-suicide_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-suicide.csv make_model_input-cohort_unvax-sub_covid_nonhospitalised-addiction: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-addiction + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-addiction needs: - stage1_data_cleaning_all outputs: @@ -3203,7 +3239,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_nonhospitalised-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-addiction.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-addiction.csv @@ -3214,7 +3250,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-addiction.csv make_model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -3224,7 +3260,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-anxiety_general.csv @@ -3235,7 +3271,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-anxiety_general.csv make_model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: @@ -3245,7 +3281,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd.csv @@ -3256,7 +3292,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd.csv make_model_input-cohort_unvax-sub_covid_nonhospitalised-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-depression needs: - stage1_data_cleaning_all outputs: @@ -3266,7 +3302,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_nonhospitalised-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-depression.csv @@ -3277,7 +3313,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-depression.csv make_model_input-cohort_unvax-sub_covid_nonhospitalised-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-eating_disorders + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-eating_disorders needs: - stage1_data_cleaning_all outputs: @@ -3287,7 +3323,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_nonhospitalised-eating_disorders: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-eating_disorders.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-eating_disorders.csv @@ -3298,7 +3334,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-eating_disorders.csv make_model_input-cohort_unvax-sub_covid_nonhospitalised-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-self_harm + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-self_harm needs: - stage1_data_cleaning_all outputs: @@ -3308,7 +3344,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_nonhospitalised-self_harm: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-self_harm.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-self_harm.csv @@ -3319,7 +3355,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-self_harm.csv make_model_input-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -3329,7 +3365,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness.csv @@ -3340,7 +3376,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness.csv make_model_input-cohort_unvax-sub_covid_nonhospitalised-suicide: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-suicide + run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-suicide needs: - stage1_data_cleaning_all outputs: @@ -3350,7 +3386,7 @@ actions: cox_ipw-cohort_unvax-sub_covid_nonhospitalised-suicide: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-suicide.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-suicide.csv @@ -3361,7 +3397,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-suicide.csv make_model_input-cohort_vax-sub_covid_nonhospitalised-addiction: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_nonhospitalised-addiction + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-addiction needs: - stage1_data_cleaning_all outputs: @@ -3371,7 +3407,7 @@ actions: cox_ipw-cohort_vax-sub_covid_nonhospitalised-addiction: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-addiction.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-addiction.csv @@ -3382,7 +3418,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-addiction.csv make_model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_nonhospitalised-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -3392,7 +3428,7 @@ actions: cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-anxiety_general.csv @@ -3403,7 +3439,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-anxiety_general.csv make_model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd needs: - stage1_data_cleaning_all outputs: @@ -3413,7 +3449,7 @@ actions: cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd.csv @@ -3424,7 +3460,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd.csv make_model_input-cohort_vax-sub_covid_nonhospitalised-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_nonhospitalised-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-depression needs: - stage1_data_cleaning_all outputs: @@ -3434,7 +3470,7 @@ actions: cox_ipw-cohort_vax-sub_covid_nonhospitalised-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-depression.csv @@ -3445,7 +3481,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-depression.csv make_model_input-cohort_vax-sub_covid_nonhospitalised-eating_disorders: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_nonhospitalised-eating_disorders + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-eating_disorders needs: - stage1_data_cleaning_all outputs: @@ -3455,7 +3491,7 @@ actions: cox_ipw-cohort_vax-sub_covid_nonhospitalised-eating_disorders: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-eating_disorders.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-eating_disorders.csv @@ -3466,7 +3502,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-eating_disorders.csv make_model_input-cohort_vax-sub_covid_nonhospitalised-self_harm: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_nonhospitalised-self_harm + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-self_harm needs: - stage1_data_cleaning_all outputs: @@ -3476,7 +3512,7 @@ actions: cox_ipw-cohort_vax-sub_covid_nonhospitalised-self_harm: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-self_harm.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-self_harm.csv @@ -3487,7 +3523,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-self_harm.csv make_model_input-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_nonhospitalised-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -3497,7 +3533,7 @@ actions: cox_ipw-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness.csv @@ -3508,7 +3544,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness.csv make_model_input-cohort_vax-sub_covid_nonhospitalised-suicide: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_nonhospitalised-suicide + run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-suicide needs: - stage1_data_cleaning_all outputs: @@ -3518,7 +3554,7 @@ actions: cox_ipw-cohort_vax-sub_covid_nonhospitalised-suicide: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-suicide.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-suicide.csv @@ -3529,7 +3565,7 @@ actions: model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-suicide.csv make_model_input-cohort_prevax-sub_ethnicity_asian-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_asian-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_asian-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -3539,7 +3575,7 @@ actions: cox_ipw-cohort_prevax-sub_ethnicity_asian-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-anxiety_general.csv @@ -3549,113 +3585,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_asian-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_asian-anxiety_general_extf + make_model_input-cohort_prevax-sub_ethnicity_asian-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_asian-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_asian-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_asian-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_asian-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_ethnicity_asian-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_asian-anxiety_general_extf + - make_model_input-cohort_prevax-sub_ethnicity_asian-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_asian-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_asian-depression + make_model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_asian-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_asian-depression.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_asian-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-depression.rds + cox_ipw-cohort_prevax-sub_ethnicity_asian-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_asian-depression + - make_model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-depression.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_ethnicity_asian-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_asian-depression_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_asian-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_asian-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_asian-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_asian-anxiety_general.rds - cox_ipw-cohort_prevax-sub_ethnicity_asian-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_asian-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_asian-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_asian-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_asian-depression_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_asian-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_asian-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_asian-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_ethnicity_asian-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_asian-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_asian-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_asian-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_asian-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_asian-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_asian-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_ethnicity_asian-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_asian-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_asian-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_asian-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness.csv make_model_input-cohort_unvax-sub_ethnicity_asian-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_asian-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_asian-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -3665,7 +3701,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_asian-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_asian-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_asian-anxiety_general.csv @@ -3676,7 +3712,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_asian-anxiety_general.csv make_model_input-cohort_unvax-sub_ethnicity_asian-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_asian-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_asian-depression needs: - stage1_data_cleaning_all outputs: @@ -3686,7 +3722,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_asian-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_asian-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_asian-depression.csv @@ -3697,7 +3733,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_asian-depression.csv make_model_input-cohort_unvax-sub_ethnicity_asian-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_asian-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_asian-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -3707,7 +3743,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_asian-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_asian-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_asian-serious_mental_illness.csv @@ -3718,7 +3754,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_asian-serious_mental_illness.csv make_model_input-cohort_vax-sub_ethnicity_asian-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_asian-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_asian-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -3728,7 +3764,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_asian-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_asian-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_asian-anxiety_general.csv @@ -3739,7 +3775,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_asian-anxiety_general.csv make_model_input-cohort_vax-sub_ethnicity_asian-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_asian-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_asian-depression needs: - stage1_data_cleaning_all outputs: @@ -3749,7 +3785,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_asian-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_asian-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_asian-depression.csv @@ -3760,7 +3796,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_asian-depression.csv make_model_input-cohort_vax-sub_ethnicity_asian-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_asian-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_asian-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -3770,7 +3806,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_asian-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_asian-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_asian-serious_mental_illness.csv @@ -3781,7 +3817,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_asian-serious_mental_illness.csv make_model_input-cohort_prevax-sub_ethnicity_black-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_black-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_black-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -3791,7 +3827,7 @@ actions: cox_ipw-cohort_prevax-sub_ethnicity_black-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_black-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-anxiety_general.csv @@ -3801,113 +3837,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_ethnicity_black-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_black-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_black-anxiety_general_extf + make_model_input-cohort_prevax-sub_ethnicity_black-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_black-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_black-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_black-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_black-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_black-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_ethnicity_black-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_black-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_black-anxiety_general_extf + - make_model_input-cohort_prevax-sub_ethnicity_black-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_black-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_black-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_black-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_black-depression + make_model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_black-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_black-depression.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_black-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_black-depression.rds + cox_ipw-cohort_prevax-sub_ethnicity_black-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_black-depression + - make_model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_black-depression.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_black-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_ethnicity_black-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_black-depression_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_black-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_black-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_black-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_black-anxiety_general.rds - cox_ipw-cohort_prevax-sub_ethnicity_black-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_black-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_black-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_black-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_black-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_black-depression_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_black-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_black-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_black-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_black-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_ethnicity_black-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_black-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_black-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_black-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_black-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_black-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_black-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_ethnicity_black-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_black-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_black-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_black-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_black-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_black-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness.csv make_model_input-cohort_unvax-sub_ethnicity_black-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_black-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_black-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -3917,7 +3953,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_black-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_black-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_black-anxiety_general.csv @@ -3928,7 +3964,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_black-anxiety_general.csv make_model_input-cohort_unvax-sub_ethnicity_black-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_black-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_black-depression needs: - stage1_data_cleaning_all outputs: @@ -3938,7 +3974,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_black-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_black-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_black-depression.csv @@ -3949,7 +3985,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_black-depression.csv make_model_input-cohort_unvax-sub_ethnicity_black-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_black-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_black-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -3959,7 +3995,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_black-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_black-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_black-serious_mental_illness.csv @@ -3970,7 +4006,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_black-serious_mental_illness.csv make_model_input-cohort_vax-sub_ethnicity_black-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_black-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_black-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -3980,7 +4016,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_black-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_black-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_black-anxiety_general.csv @@ -3991,7 +4027,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_black-anxiety_general.csv make_model_input-cohort_vax-sub_ethnicity_black-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_black-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_black-depression needs: - stage1_data_cleaning_all outputs: @@ -4001,7 +4037,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_black-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_black-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_black-depression.csv @@ -4012,7 +4048,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_black-depression.csv make_model_input-cohort_vax-sub_ethnicity_black-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_black-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_black-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -4022,7 +4058,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_black-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_black-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_black-serious_mental_illness.csv @@ -4033,7 +4069,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_black-serious_mental_illness.csv make_model_input-cohort_prevax-sub_ethnicity_mixed-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_mixed-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_mixed-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4043,7 +4079,7 @@ actions: cox_ipw-cohort_prevax-sub_ethnicity_mixed-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-anxiety_general.csv @@ -4053,113 +4089,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_mixed-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_mixed-anxiety_general_extf + make_model_input-cohort_prevax-sub_ethnicity_mixed-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_mixed-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_mixed-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_mixed-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_mixed-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_ethnicity_mixed-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_mixed-anxiety_general_extf + - make_model_input-cohort_prevax-sub_ethnicity_mixed-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_mixed-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_mixed-depression + make_model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_mixed-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_mixed-depression.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_mixed-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-depression.rds + cox_ipw-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_mixed-depression + - make_model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-depression.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_ethnicity_mixed-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_mixed-depression_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_mixed-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_mixed-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_mixed-anxiety_general.rds - cox_ipw-cohort_prevax-sub_ethnicity_mixed-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_mixed-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_mixed-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_mixed-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_mixed-depression_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_mixed-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_mixed-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_mixed-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_mixed-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_mixed-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_mixed-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_mixed-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_mixed-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_mixed-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness.csv make_model_input-cohort_unvax-sub_ethnicity_mixed-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_mixed-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_mixed-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4169,7 +4205,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_mixed-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_mixed-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_mixed-anxiety_general.csv @@ -4180,7 +4216,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_mixed-anxiety_general.csv make_model_input-cohort_unvax-sub_ethnicity_mixed-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_mixed-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_mixed-depression needs: - stage1_data_cleaning_all outputs: @@ -4190,7 +4226,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_mixed-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_mixed-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_mixed-depression.csv @@ -4201,7 +4237,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_mixed-depression.csv make_model_input-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_mixed-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_mixed-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -4211,7 +4247,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness.csv @@ -4222,7 +4258,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness.csv make_model_input-cohort_vax-sub_ethnicity_mixed-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_mixed-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_mixed-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4232,7 +4268,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_mixed-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_mixed-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_mixed-anxiety_general.csv @@ -4243,7 +4279,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_mixed-anxiety_general.csv make_model_input-cohort_vax-sub_ethnicity_mixed-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_mixed-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_mixed-depression needs: - stage1_data_cleaning_all outputs: @@ -4253,7 +4289,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_mixed-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_mixed-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_mixed-depression.csv @@ -4264,7 +4300,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_mixed-depression.csv make_model_input-cohort_vax-sub_ethnicity_mixed-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_mixed-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_mixed-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -4274,7 +4310,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_mixed-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_mixed-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_mixed-serious_mental_illness.csv @@ -4285,7 +4321,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_mixed-serious_mental_illness.csv make_model_input-cohort_prevax-sub_ethnicity_other-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_other-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_other-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4295,7 +4331,7 @@ actions: cox_ipw-cohort_prevax-sub_ethnicity_other-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_other-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-anxiety_general.csv @@ -4305,113 +4341,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_ethnicity_other-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_other-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_other-anxiety_general_extf + make_model_input-cohort_prevax-sub_ethnicity_other-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_other-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_other-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_other-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_other-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_other-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_ethnicity_other-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_other-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_other-anxiety_general_extf + - make_model_input-cohort_prevax-sub_ethnicity_other-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_other-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_other-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_other-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_other-depression + make_model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_other-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_other-depression.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_other-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_other-depression.rds + cox_ipw-cohort_prevax-sub_ethnicity_other-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_other-depression + - make_model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_other-depression.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_other-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_ethnicity_other-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_other-depression_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_other-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_other-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_other-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_other-anxiety_general.rds - cox_ipw-cohort_prevax-sub_ethnicity_other-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_other-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_other-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_other-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_other-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_other-depression_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_other-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_other-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_other-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_other-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_ethnicity_other-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_other-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_other-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_other-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_other-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_other-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_other-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_ethnicity_other-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_other-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_other-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_other-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_other-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_other-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness.csv make_model_input-cohort_unvax-sub_ethnicity_other-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_other-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_other-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4421,7 +4457,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_other-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_other-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_other-anxiety_general.csv @@ -4432,7 +4468,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_other-anxiety_general.csv make_model_input-cohort_unvax-sub_ethnicity_other-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_other-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_other-depression needs: - stage1_data_cleaning_all outputs: @@ -4442,7 +4478,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_other-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_other-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_other-depression.csv @@ -4453,7 +4489,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_other-depression.csv make_model_input-cohort_unvax-sub_ethnicity_other-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_other-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_other-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -4463,7 +4499,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_other-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_other-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_other-serious_mental_illness.csv @@ -4474,7 +4510,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_other-serious_mental_illness.csv make_model_input-cohort_vax-sub_ethnicity_other-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_other-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_other-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4484,7 +4520,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_other-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_other-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_other-anxiety_general.csv @@ -4495,7 +4531,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_other-anxiety_general.csv make_model_input-cohort_vax-sub_ethnicity_other-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_other-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_other-depression needs: - stage1_data_cleaning_all outputs: @@ -4505,7 +4541,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_other-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_other-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_other-depression.csv @@ -4516,7 +4552,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_other-depression.csv make_model_input-cohort_vax-sub_ethnicity_other-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_other-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_other-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -4526,7 +4562,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_other-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_other-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_other-serious_mental_illness.csv @@ -4537,7 +4573,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_other-serious_mental_illness.csv make_model_input-cohort_prevax-sub_ethnicity_white-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_white-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_white-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4547,7 +4583,7 @@ actions: cox_ipw-cohort_prevax-sub_ethnicity_white-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_white-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-anxiety_general.csv @@ -4557,113 +4593,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_ethnicity_white-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_white-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_white-anxiety_general_extf + make_model_input-cohort_prevax-sub_ethnicity_white-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_white-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_white-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_white-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_white-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_white-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_ethnicity_white-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_white-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_white-anxiety_general_extf + - make_model_input-cohort_prevax-sub_ethnicity_white-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_white-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_white-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_white-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_white-depression + make_model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_ethnicity_white-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_white-depression.rds + model_input: output/model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_white-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_white-depression.rds + cox_ipw-cohort_prevax-sub_ethnicity_white-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_white-depression + - make_model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_white-depression.csv + model_output: output/model_output-cohort_prevax-sub_ethnicity_white-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_ethnicity_white-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_white-depression_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_white-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_white-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_white-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_white-anxiety_general.rds - cox_ipw-cohort_prevax-sub_ethnicity_white-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_white-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_white-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_white-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_white-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_white-depression_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_white-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_white-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_white-anxiety_general.csv - make_model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_white-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_ethnicity_white-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_white-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_white-depression.rds - cox_ipw-cohort_prevax-sub_ethnicity_white-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_white-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_white-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_white-depression.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_ethnicity_white-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_white-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_white-depression.csv - make_model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_ethnicity_white-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_ethnicity_white-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_ethnicity_white-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness.csv make_model_input-cohort_unvax-sub_ethnicity_white-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_white-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_white-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4673,7 +4709,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_white-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_white-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_white-anxiety_general.csv @@ -4684,7 +4720,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_white-anxiety_general.csv make_model_input-cohort_unvax-sub_ethnicity_white-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_white-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_white-depression needs: - stage1_data_cleaning_all outputs: @@ -4694,7 +4730,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_white-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_white-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_white-depression.csv @@ -4705,7 +4741,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_white-depression.csv make_model_input-cohort_unvax-sub_ethnicity_white-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_ethnicity_white-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_white-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -4715,7 +4751,7 @@ actions: cox_ipw-cohort_unvax-sub_ethnicity_white-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_ethnicity_white-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_white-serious_mental_illness.csv @@ -4726,7 +4762,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_ethnicity_white-serious_mental_illness.csv make_model_input-cohort_vax-sub_ethnicity_white-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_white-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_white-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -4736,7 +4772,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_white-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_white-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_white-anxiety_general.csv @@ -4747,7 +4783,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_white-anxiety_general.csv make_model_input-cohort_vax-sub_ethnicity_white-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_white-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_white-depression needs: - stage1_data_cleaning_all outputs: @@ -4757,7 +4793,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_white-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_white-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_white-depression.csv @@ -4768,7 +4804,7 @@ actions: model_output: output/model_output-cohort_vax-sub_ethnicity_white-depression.csv make_model_input-cohort_vax-sub_ethnicity_white-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_ethnicity_white-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_white-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -4778,7 +4814,7 @@ actions: cox_ipw-cohort_vax-sub_ethnicity_white-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_ethnicity_white-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_white-serious_mental_illness.csv @@ -4788,764 +4824,764 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_vax-sub_ethnicity_white-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_priorhistory_none-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_none-anxiety_general + make_model_input-cohort_prevax-sub_history_none-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_none-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_none-anxiety_general.rds + model_input: output/model_input-cohort_prevax-sub_history_none-anxiety_general.rds - cox_ipw-cohort_prevax-sub_priorhistory_none-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_none-anxiety_general.rds + cox_ipw-cohort_prevax-sub_history_none-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_none-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_none-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_none-anxiety_general + - make_model_input-cohort_prevax-sub_history_none-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_none-anxiety_general.csv + model_output: output/model_output-cohort_prevax-sub_history_none-anxiety_general.csv - make_model_input-cohort_prevax-sub_priorhistory_none-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_none-anxiety_general_extf + make_model_input-cohort_prevax-sub_history_none-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_none-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_none-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_history_none-depression.rds - cox_ipw-cohort_prevax-sub_priorhistory_none-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_none-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_history_none-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_none-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_none-depression.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_none-anxiety_general_extf + - make_model_input-cohort_prevax-sub_history_none-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_none-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_history_none-depression.csv - make_model_input-cohort_prevax-sub_priorhistory_none-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_none-depression + make_model_input-cohort_prevax-sub_history_none-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_none-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_none-depression.rds + model_input: output/model_input-cohort_prevax-sub_history_none-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_priorhistory_none-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_none-depression.rds + cox_ipw-cohort_prevax-sub_history_none-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_none-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_none-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_none-depression + - make_model_input-cohort_prevax-sub_history_none-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_none-depression.csv + model_output: output/model_output-cohort_prevax-sub_history_none-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_priorhistory_none-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_none-depression_extf + make_model_input-cohort_prevax_extf-sub_history_none-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_none-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_none-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_none-anxiety_general.rds - cox_ipw-cohort_prevax-sub_priorhistory_none-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_none-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_history_none-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_none-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_none-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_none-depression_extf + - make_model_input-cohort_prevax_extf-sub_history_none-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_none-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_none-anxiety_general.csv - make_model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_none-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_history_none-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_none-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_none-depression.rds - cox_ipw-cohort_prevax-sub_priorhistory_none-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_history_none-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_none-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_none-depression.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_history_none-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_none-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_none-depression.csv - make_model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_none-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_history_none-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_none-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_none-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_priorhistory_none-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_history_none-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_none-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_none-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_history_none-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_none-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_none-serious_mental_illness.csv - make_model_input-cohort_unvax-sub_priorhistory_none-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_none-anxiety_general + make_model_input-cohort_unvax-sub_history_none-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_none-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_none-anxiety_general.rds + model_input: output/model_input-cohort_unvax-sub_history_none-anxiety_general.rds - cox_ipw-cohort_unvax-sub_priorhistory_none-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_none-anxiety_general.rds + cox_ipw-cohort_unvax-sub_history_none-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_none-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_none-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_none-anxiety_general.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_none-anxiety_general + - make_model_input-cohort_unvax-sub_history_none-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_none-anxiety_general.csv + model_output: output/model_output-cohort_unvax-sub_history_none-anxiety_general.csv - make_model_input-cohort_unvax-sub_priorhistory_none-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_none-depression + make_model_input-cohort_unvax-sub_history_none-depression: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_none-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_none-depression.rds + model_input: output/model_input-cohort_unvax-sub_history_none-depression.rds - cox_ipw-cohort_unvax-sub_priorhistory_none-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_none-depression.rds + cox_ipw-cohort_unvax-sub_history_none-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_none-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_none-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_none-depression.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_none-depression + - make_model_input-cohort_unvax-sub_history_none-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_none-depression.csv + model_output: output/model_output-cohort_unvax-sub_history_none-depression.csv - make_model_input-cohort_unvax-sub_priorhistory_none-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_none-serious_mental_illness + make_model_input-cohort_unvax-sub_history_none-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_none-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_none-serious_mental_illness.rds + model_input: output/model_input-cohort_unvax-sub_history_none-serious_mental_illness.rds - cox_ipw-cohort_unvax-sub_priorhistory_none-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_none-serious_mental_illness.rds + cox_ipw-cohort_unvax-sub_history_none-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_none-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_none-serious_mental_illness.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_none-serious_mental_illness.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_none-serious_mental_illness + - make_model_input-cohort_unvax-sub_history_none-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_none-serious_mental_illness.csv + model_output: output/model_output-cohort_unvax-sub_history_none-serious_mental_illness.csv - make_model_input-cohort_vax-sub_priorhistory_none-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_none-anxiety_general + make_model_input-cohort_vax-sub_history_none-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_none-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_none-anxiety_general.rds + model_input: output/model_input-cohort_vax-sub_history_none-anxiety_general.rds - cox_ipw-cohort_vax-sub_priorhistory_none-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_none-anxiety_general.rds + cox_ipw-cohort_vax-sub_history_none-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_none-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_none-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_none-anxiety_general.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_none-anxiety_general + - make_model_input-cohort_vax-sub_history_none-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_none-anxiety_general.csv + model_output: output/model_output-cohort_vax-sub_history_none-anxiety_general.csv - make_model_input-cohort_vax-sub_priorhistory_none-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_none-depression + make_model_input-cohort_vax-sub_history_none-depression: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_none-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_none-depression.rds + model_input: output/model_input-cohort_vax-sub_history_none-depression.rds - cox_ipw-cohort_vax-sub_priorhistory_none-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_none-depression.rds + cox_ipw-cohort_vax-sub_history_none-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_none-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_none-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_none-depression.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_none-depression + - make_model_input-cohort_vax-sub_history_none-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_none-depression.csv + model_output: output/model_output-cohort_vax-sub_history_none-depression.csv - make_model_input-cohort_vax-sub_priorhistory_none-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_none-serious_mental_illness + make_model_input-cohort_vax-sub_history_none-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_none-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_none-serious_mental_illness.rds + model_input: output/model_input-cohort_vax-sub_history_none-serious_mental_illness.rds - cox_ipw-cohort_vax-sub_priorhistory_none-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_none-serious_mental_illness.rds + cox_ipw-cohort_vax-sub_history_none-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_none-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_none-serious_mental_illness.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_none-serious_mental_illness.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_none-serious_mental_illness + - make_model_input-cohort_vax-sub_history_none-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_none-serious_mental_illness.csv + model_output: output/model_output-cohort_vax-sub_history_none-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_notrecent-anxiety_general + make_model_input-cohort_prevax-sub_history_notrecent-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_notrecent-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general.rds + model_input: output/model_input-cohort_prevax-sub_history_notrecent-anxiety_general.rds - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general.rds + cox_ipw-cohort_prevax-sub_history_notrecent-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_notrecent-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_notrecent-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general + - make_model_input-cohort_prevax-sub_history_notrecent-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-anxiety_general.csv + model_output: output/model_output-cohort_prevax-sub_history_notrecent-anxiety_general.csv - make_model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_notrecent-anxiety_general_extf + make_model_input-cohort_prevax-sub_history_notrecent-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_notrecent-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_history_notrecent-depression.rds - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_history_notrecent-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_notrecent-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_notrecent-depression.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general_extf + - make_model_input-cohort_prevax-sub_history_notrecent-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_history_notrecent-depression.csv - make_model_input-cohort_prevax-sub_priorhistory_notrecent-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_notrecent-depression + make_model_input-cohort_prevax-sub_history_notrecent-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_notrecent-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_notrecent-depression.rds + model_input: output/model_input-cohort_prevax-sub_history_notrecent-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-depression.rds + cox_ipw-cohort_prevax-sub_history_notrecent-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_notrecent-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_notrecent-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_notrecent-depression + - make_model_input-cohort_prevax-sub_history_notrecent-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-depression.csv + model_output: output/model_output-cohort_prevax-sub_history_notrecent-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_priorhistory_notrecent-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_notrecent-depression_extf + make_model_input-cohort_prevax_extf-sub_history_notrecent-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_notrecent-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_notrecent-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_notrecent-anxiety_general.rds - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_history_notrecent-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_notrecent-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_notrecent-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_notrecent-depression_extf + - make_model_input-cohort_prevax_extf-sub_history_notrecent-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_notrecent-anxiety_general.csv - make_model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_history_notrecent-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_notrecent-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_notrecent-depression.rds - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_history_notrecent-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_notrecent-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_notrecent-depression.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_history_notrecent-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_notrecent-depression.csv - make_model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_notrecent-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness.csv - make_model_input-cohort_unvax-sub_priorhistory_notrecent-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_notrecent-anxiety_general + make_model_input-cohort_unvax-sub_history_notrecent-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_notrecent-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_notrecent-anxiety_general.rds + model_input: output/model_input-cohort_unvax-sub_history_notrecent-anxiety_general.rds - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_notrecent-anxiety_general.rds + cox_ipw-cohort_unvax-sub_history_notrecent-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_notrecent-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_notrecent-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_notrecent-anxiety_general.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_notrecent-anxiety_general + - make_model_input-cohort_unvax-sub_history_notrecent-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_notrecent-anxiety_general.csv + model_output: output/model_output-cohort_unvax-sub_history_notrecent-anxiety_general.csv - make_model_input-cohort_unvax-sub_priorhistory_notrecent-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_notrecent-depression + make_model_input-cohort_unvax-sub_history_notrecent-depression: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_notrecent-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_notrecent-depression.rds + model_input: output/model_input-cohort_unvax-sub_history_notrecent-depression.rds - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_notrecent-depression.rds + cox_ipw-cohort_unvax-sub_history_notrecent-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_notrecent-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_notrecent-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_notrecent-depression.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_notrecent-depression + - make_model_input-cohort_unvax-sub_history_notrecent-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_notrecent-depression.csv + model_output: output/model_output-cohort_unvax-sub_history_notrecent-depression.csv - make_model_input-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness + make_model_input-cohort_unvax-sub_history_notrecent-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_notrecent-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness.rds + model_input: output/model_input-cohort_unvax-sub_history_notrecent-serious_mental_illness.rds - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness.rds + cox_ipw-cohort_unvax-sub_history_notrecent-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_notrecent-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_notrecent-serious_mental_illness.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness + - make_model_input-cohort_unvax-sub_history_notrecent-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness.csv + model_output: output/model_output-cohort_unvax-sub_history_notrecent-serious_mental_illness.csv - make_model_input-cohort_vax-sub_priorhistory_notrecent-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_notrecent-anxiety_general + make_model_input-cohort_vax-sub_history_notrecent-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_notrecent-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_notrecent-anxiety_general.rds + model_input: output/model_input-cohort_vax-sub_history_notrecent-anxiety_general.rds - cox_ipw-cohort_vax-sub_priorhistory_notrecent-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_notrecent-anxiety_general.rds + cox_ipw-cohort_vax-sub_history_notrecent-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_notrecent-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_notrecent-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_notrecent-anxiety_general.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_notrecent-anxiety_general + - make_model_input-cohort_vax-sub_history_notrecent-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_notrecent-anxiety_general.csv + model_output: output/model_output-cohort_vax-sub_history_notrecent-anxiety_general.csv - make_model_input-cohort_vax-sub_priorhistory_notrecent-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_notrecent-depression + make_model_input-cohort_vax-sub_history_notrecent-depression: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_notrecent-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_notrecent-depression.rds + model_input: output/model_input-cohort_vax-sub_history_notrecent-depression.rds - cox_ipw-cohort_vax-sub_priorhistory_notrecent-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_notrecent-depression.rds + cox_ipw-cohort_vax-sub_history_notrecent-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_notrecent-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_notrecent-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_notrecent-depression.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_notrecent-depression + - make_model_input-cohort_vax-sub_history_notrecent-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_notrecent-depression.csv + model_output: output/model_output-cohort_vax-sub_history_notrecent-depression.csv - make_model_input-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_notrecent-serious_mental_illness + make_model_input-cohort_vax-sub_history_notrecent-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_notrecent-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness.rds + model_input: output/model_input-cohort_vax-sub_history_notrecent-serious_mental_illness.rds - cox_ipw-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness.rds + cox_ipw-cohort_vax-sub_history_notrecent-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_notrecent-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_notrecent-serious_mental_illness.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness + - make_model_input-cohort_vax-sub_history_notrecent-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness.csv + model_output: output/model_output-cohort_vax-sub_history_notrecent-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_recent-anxiety_general + make_model_input-cohort_prevax-sub_history_recent-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_recent-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general.rds + model_input: output/model_input-cohort_prevax-sub_history_recent-anxiety_general.rds - cox_ipw-cohort_prevax-sub_priorhistory_recent-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general.rds + cox_ipw-cohort_prevax-sub_history_recent-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_recent-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_recent-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general + - make_model_input-cohort_prevax-sub_history_recent-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-anxiety_general.csv + model_output: output/model_output-cohort_prevax-sub_history_recent-anxiety_general.csv - make_model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_recent-anxiety_general_extf + make_model_input-cohort_prevax-sub_history_recent-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_recent-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_history_recent-depression.rds - cox_ipw-cohort_prevax-sub_priorhistory_recent-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_history_recent-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_recent-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_recent-depression.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general_extf + - make_model_input-cohort_prevax-sub_history_recent-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_history_recent-depression.csv - make_model_input-cohort_prevax-sub_priorhistory_recent-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_recent-depression + make_model_input-cohort_prevax-sub_history_recent-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_history_recent-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_recent-depression.rds + model_input: output/model_input-cohort_prevax-sub_history_recent-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_priorhistory_recent-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-depression.rds + cox_ipw-cohort_prevax-sub_history_recent-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_history_recent-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_history_recent-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_recent-depression + - make_model_input-cohort_prevax-sub_history_recent-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-depression.csv + model_output: output/model_output-cohort_prevax-sub_history_recent-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_priorhistory_recent-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_recent-depression_extf + make_model_input-cohort_prevax_extf-sub_history_recent-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_recent-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_recent-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_recent-anxiety_general.rds - cox_ipw-cohort_prevax-sub_priorhistory_recent-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_history_recent-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_recent-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_recent-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_recent-depression_extf + - make_model_input-cohort_prevax_extf-sub_history_recent-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_recent-anxiety_general.csv - make_model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_recent-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_history_recent-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_recent-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_recent-depression.rds - cox_ipw-cohort_prevax-sub_priorhistory_recent-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_history_recent-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_recent-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_recent-depression.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_history_recent-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_recent-depression.csv - make_model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_priorhistory_recent-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_history_recent-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_recent-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_history_recent-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_priorhistory_recent-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_history_recent-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_history_recent-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_recent-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_history_recent-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_history_recent-serious_mental_illness.csv - make_model_input-cohort_unvax-sub_priorhistory_recent-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_recent-anxiety_general + make_model_input-cohort_unvax-sub_history_recent-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_recent-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_recent-anxiety_general.rds + model_input: output/model_input-cohort_unvax-sub_history_recent-anxiety_general.rds - cox_ipw-cohort_unvax-sub_priorhistory_recent-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_recent-anxiety_general.rds + cox_ipw-cohort_unvax-sub_history_recent-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_recent-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_recent-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_recent-anxiety_general.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_recent-anxiety_general + - make_model_input-cohort_unvax-sub_history_recent-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_recent-anxiety_general.csv + model_output: output/model_output-cohort_unvax-sub_history_recent-anxiety_general.csv - make_model_input-cohort_unvax-sub_priorhistory_recent-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_recent-depression + make_model_input-cohort_unvax-sub_history_recent-depression: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_recent-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_recent-depression.rds + model_input: output/model_input-cohort_unvax-sub_history_recent-depression.rds - cox_ipw-cohort_unvax-sub_priorhistory_recent-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_recent-depression.rds + cox_ipw-cohort_unvax-sub_history_recent-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_recent-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_recent-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_recent-depression.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_recent-depression + - make_model_input-cohort_unvax-sub_history_recent-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_recent-depression.csv + model_output: output/model_output-cohort_unvax-sub_history_recent-depression.csv - make_model_input-cohort_unvax-sub_priorhistory_recent-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_priorhistory_recent-serious_mental_illness + make_model_input-cohort_unvax-sub_history_recent-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_unvax-sub_history_recent-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_unvax-sub_priorhistory_recent-serious_mental_illness.rds + model_input: output/model_input-cohort_unvax-sub_history_recent-serious_mental_illness.rds - cox_ipw-cohort_unvax-sub_priorhistory_recent-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_priorhistory_recent-serious_mental_illness.rds + cox_ipw-cohort_unvax-sub_history_recent-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_history_recent-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_recent-serious_mental_illness.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_history_recent-serious_mental_illness.csv needs: - - make_model_input-cohort_unvax-sub_priorhistory_recent-serious_mental_illness + - make_model_input-cohort_unvax-sub_history_recent-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_unvax-sub_priorhistory_recent-serious_mental_illness.csv + model_output: output/model_output-cohort_unvax-sub_history_recent-serious_mental_illness.csv - make_model_input-cohort_vax-sub_priorhistory_recent-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_recent-anxiety_general + make_model_input-cohort_vax-sub_history_recent-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_recent-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_recent-anxiety_general.rds + model_input: output/model_input-cohort_vax-sub_history_recent-anxiety_general.rds - cox_ipw-cohort_vax-sub_priorhistory_recent-anxiety_general: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_recent-anxiety_general.rds + cox_ipw-cohort_vax-sub_history_recent-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_recent-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_recent-anxiety_general.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_recent-anxiety_general.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_recent-anxiety_general + - make_model_input-cohort_vax-sub_history_recent-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_recent-anxiety_general.csv + model_output: output/model_output-cohort_vax-sub_history_recent-anxiety_general.csv - make_model_input-cohort_vax-sub_priorhistory_recent-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_recent-depression + make_model_input-cohort_vax-sub_history_recent-depression: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_recent-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_recent-depression.rds + model_input: output/model_input-cohort_vax-sub_history_recent-depression.rds - cox_ipw-cohort_vax-sub_priorhistory_recent-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_recent-depression.rds + cox_ipw-cohort_vax-sub_history_recent-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_recent-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_recent-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_recent-depression.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_recent-depression + - make_model_input-cohort_vax-sub_history_recent-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_recent-depression.csv + model_output: output/model_output-cohort_vax-sub_history_recent-depression.csv - make_model_input-cohort_vax-sub_priorhistory_recent-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_priorhistory_recent-serious_mental_illness + make_model_input-cohort_vax-sub_history_recent-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_vax-sub_history_recent-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_vax-sub_priorhistory_recent-serious_mental_illness.rds + model_input: output/model_input-cohort_vax-sub_history_recent-serious_mental_illness.rds - cox_ipw-cohort_vax-sub_priorhistory_recent-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_priorhistory_recent-serious_mental_illness.rds + cox_ipw-cohort_vax-sub_history_recent-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_history_recent-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_recent-serious_mental_illness.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_history_recent-serious_mental_illness.csv needs: - - make_model_input-cohort_vax-sub_priorhistory_recent-serious_mental_illness + - make_model_input-cohort_vax-sub_history_recent-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_vax-sub_priorhistory_recent-serious_mental_illness.csv + model_output: output/model_output-cohort_vax-sub_history_recent-serious_mental_illness.csv make_model_input-cohort_prevax-sub_sex_female-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_female-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_sex_female-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -5555,7 +5591,7 @@ actions: cox_ipw-cohort_prevax-sub_sex_female-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_female-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-anxiety_general.csv @@ -5565,113 +5601,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_sex_female-anxiety_general.csv - make_model_input-cohort_prevax-sub_sex_female-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_female-anxiety_general_extf + make_model_input-cohort_prevax-sub_sex_female-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_sex_female-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_female-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_sex_female-depression.rds - cox_ipw-cohort_prevax-sub_sex_female-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_female-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_sex_female-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_female-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-depression.csv needs: - - make_model_input-cohort_prevax-sub_sex_female-anxiety_general_extf + - make_model_input-cohort_prevax-sub_sex_female-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_female-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_sex_female-depression.csv - make_model_input-cohort_prevax-sub_sex_female-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_female-depression + make_model_input-cohort_prevax-sub_sex_female-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_sex_female-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_female-depression.rds + model_input: output/model_input-cohort_prevax-sub_sex_female-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_sex_female-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_female-depression.rds + cox_ipw-cohort_prevax-sub_sex_female-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_female-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_sex_female-depression + - make_model_input-cohort_prevax-sub_sex_female-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_female-depression.csv + model_output: output/model_output-cohort_prevax-sub_sex_female-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_sex_female-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_female-depression_extf + make_model_input-cohort_prevax_extf-sub_sex_female-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_female-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_female-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_sex_female-anxiety_general.rds - cox_ipw-cohort_prevax-sub_sex_female-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_female-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_sex_female-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_sex_female-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_female-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_sex_female-depression_extf + - make_model_input-cohort_prevax_extf-sub_sex_female-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_female-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_sex_female-anxiety_general.csv - make_model_input-cohort_prevax-sub_sex_female-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_female-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_sex_female-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_female-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_female-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_sex_female-depression.rds - cox_ipw-cohort_prevax-sub_sex_female-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_female-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_sex_female-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_sex_female-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_female-depression.csv needs: - - make_model_input-cohort_prevax-sub_sex_female-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_sex_female-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_female-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_sex_female-depression.csv - make_model_input-cohort_prevax-sub_sex_female-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_female-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_sex_female-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_female-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_female-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_sex_female-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_sex_female-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_female-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_sex_female-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_sex_female-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_female-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_sex_female-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_sex_female-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_female-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_sex_female-serious_mental_illness.csv make_model_input-cohort_unvax-sub_sex_female-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_sex_female-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_sex_female-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -5681,7 +5717,7 @@ actions: cox_ipw-cohort_unvax-sub_sex_female-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_sex_female-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_female-anxiety_general.csv @@ -5692,7 +5728,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_sex_female-anxiety_general.csv make_model_input-cohort_unvax-sub_sex_female-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_sex_female-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_sex_female-depression needs: - stage1_data_cleaning_all outputs: @@ -5702,7 +5738,7 @@ actions: cox_ipw-cohort_unvax-sub_sex_female-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_sex_female-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_female-depression.csv @@ -5713,7 +5749,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_sex_female-depression.csv make_model_input-cohort_unvax-sub_sex_female-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_sex_female-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_sex_female-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -5723,7 +5759,7 @@ actions: cox_ipw-cohort_unvax-sub_sex_female-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_sex_female-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_female-serious_mental_illness.csv @@ -5734,7 +5770,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_sex_female-serious_mental_illness.csv make_model_input-cohort_vax-sub_sex_female-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_sex_female-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_female-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -5744,7 +5780,7 @@ actions: cox_ipw-cohort_vax-sub_sex_female-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_sex_female-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_female-anxiety_general.csv @@ -5755,7 +5791,7 @@ actions: model_output: output/model_output-cohort_vax-sub_sex_female-anxiety_general.csv make_model_input-cohort_vax-sub_sex_female-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_sex_female-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_female-depression needs: - stage1_data_cleaning_all outputs: @@ -5765,7 +5801,7 @@ actions: cox_ipw-cohort_vax-sub_sex_female-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_sex_female-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_female-depression.csv @@ -5776,7 +5812,7 @@ actions: model_output: output/model_output-cohort_vax-sub_sex_female-depression.csv make_model_input-cohort_vax-sub_sex_female-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_sex_female-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_female-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -5786,7 +5822,7 @@ actions: cox_ipw-cohort_vax-sub_sex_female-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_sex_female-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_female-serious_mental_illness.csv @@ -5797,7 +5833,7 @@ actions: model_output: output/model_output-cohort_vax-sub_sex_female-serious_mental_illness.csv make_model_input-cohort_prevax-sub_sex_male-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_male-anxiety_general + run: r:latest analysis/make_model_input.R cohort_prevax-sub_sex_male-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -5807,7 +5843,7 @@ actions: cox_ipw-cohort_prevax-sub_sex_male-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_male-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-anxiety_general.csv @@ -5817,113 +5853,113 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_prevax-sub_sex_male-anxiety_general.csv - make_model_input-cohort_prevax-sub_sex_male-anxiety_general_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_male-anxiety_general_extf + make_model_input-cohort_prevax-sub_sex_male-depression: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_sex_male-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_male-anxiety_general_extf.rds + model_input: output/model_input-cohort_prevax-sub_sex_male-depression.rds - cox_ipw-cohort_prevax-sub_sex_male-anxiety_general_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_male-anxiety_general_extf.rds + cox_ipw-cohort_prevax-sub_sex_male-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_male-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 - --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-anxiety_general_extf.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 + --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-depression.csv needs: - - make_model_input-cohort_prevax-sub_sex_male-anxiety_general_extf + - make_model_input-cohort_prevax-sub_sex_male-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_male-anxiety_general_extf.csv + model_output: output/model_output-cohort_prevax-sub_sex_male-depression.csv - make_model_input-cohort_prevax-sub_sex_male-depression: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_male-depression + make_model_input-cohort_prevax-sub_sex_male-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax-sub_sex_male-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_male-depression.rds + model_input: output/model_input-cohort_prevax-sub_sex_male-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_sex_male-depression: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_male-depression.rds + cox_ipw-cohort_prevax-sub_sex_male-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_male-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-depression.csv + --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_sex_male-depression + - make_model_input-cohort_prevax-sub_sex_male-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_male-depression.csv + model_output: output/model_output-cohort_prevax-sub_sex_male-serious_mental_illness.csv - make_model_input-cohort_prevax-sub_sex_male-depression_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_male-depression_extf + make_model_input-cohort_prevax_extf-sub_sex_male-anxiety_general: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_male-anxiety_general needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_male-depression_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_sex_male-anxiety_general.rds - cox_ipw-cohort_prevax-sub_sex_male-depression_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_male-depression_extf.rds + cox_ipw-cohort_prevax_extf-sub_sex_male-anxiety_general: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_sex_male-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-depression_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_male-anxiety_general.csv needs: - - make_model_input-cohort_prevax-sub_sex_male-depression_extf + - make_model_input-cohort_prevax_extf-sub_sex_male-anxiety_general outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_male-depression_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_sex_male-anxiety_general.csv - make_model_input-cohort_prevax-sub_sex_male-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_male-serious_mental_illness + make_model_input-cohort_prevax_extf-sub_sex_male-depression: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_male-depression needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_male-serious_mental_illness.rds + model_input: output/model_input-cohort_prevax_extf-sub_sex_male-depression.rds - cox_ipw-cohort_prevax-sub_sex_male-serious_mental_illness: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_male-serious_mental_illness.rds + cox_ipw-cohort_prevax_extf-sub_sex_male-depression: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_sex_male-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-serious_mental_illness.csv + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm + --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 + --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_male-depression.csv needs: - - make_model_input-cohort_prevax-sub_sex_male-serious_mental_illness + - make_model_input-cohort_prevax_extf-sub_sex_male-depression outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_male-serious_mental_illness.csv + model_output: output/model_output-cohort_prevax_extf-sub_sex_male-depression.csv - make_model_input-cohort_prevax-sub_sex_male-serious_mental_illness_extf: - run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_sex_male-serious_mental_illness_extf + make_model_input-cohort_prevax_extf-sub_sex_male-serious_mental_illness: + run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_male-serious_mental_illness needs: - stage1_data_cleaning_all outputs: highly_sensitive: - model_input: output/model_input-cohort_prevax-sub_sex_male-serious_mental_illness_extf.rds + model_input: output/model_input-cohort_prevax_extf-sub_sex_male-serious_mental_illness.rds - cox_ipw-cohort_prevax-sub_sex_male-serious_mental_illness_extf: - run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_sex_male-serious_mental_illness_extf.rds + cox_ipw-cohort_prevax_extf-sub_sex_male-serious_mental_illness: + run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax_extf-sub_sex_male-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50 - --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-serious_mental_illness_extf.csv + --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_male-serious_mental_illness.csv needs: - - make_model_input-cohort_prevax-sub_sex_male-serious_mental_illness_extf + - make_model_input-cohort_prevax_extf-sub_sex_male-serious_mental_illness outputs: moderately_sensitive: - model_output: output/model_output-cohort_prevax-sub_sex_male-serious_mental_illness_extf.csv + model_output: output/model_output-cohort_prevax_extf-sub_sex_male-serious_mental_illness.csv make_model_input-cohort_unvax-sub_sex_male-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_sex_male-anxiety_general + run: r:latest analysis/make_model_input.R cohort_unvax-sub_sex_male-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -5933,7 +5969,7 @@ actions: cox_ipw-cohort_unvax-sub_sex_male-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_sex_male-anxiety_general.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_male-anxiety_general.csv @@ -5944,7 +5980,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_sex_male-anxiety_general.csv make_model_input-cohort_unvax-sub_sex_male-depression: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_sex_male-depression + run: r:latest analysis/make_model_input.R cohort_unvax-sub_sex_male-depression needs: - stage1_data_cleaning_all outputs: @@ -5954,7 +5990,7 @@ actions: cox_ipw-cohort_unvax-sub_sex_male-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_sex_male-depression.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_male-depression.csv @@ -5965,7 +6001,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_sex_male-depression.csv make_model_input-cohort_unvax-sub_sex_male-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_sex_male-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_unvax-sub_sex_male-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -5975,7 +6011,7 @@ actions: cox_ipw-cohort_unvax-sub_sex_male-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_sex_male-serious_mental_illness.rds --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_male-serious_mental_illness.csv @@ -5986,7 +6022,7 @@ actions: model_output: output/model_output-cohort_unvax-sub_sex_male-serious_mental_illness.csv make_model_input-cohort_vax-sub_sex_male-anxiety_general: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_sex_male-anxiety_general + run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_male-anxiety_general needs: - stage1_data_cleaning_all outputs: @@ -5996,7 +6032,7 @@ actions: cox_ipw-cohort_vax-sub_sex_male-anxiety_general: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_sex_male-anxiety_general.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_male-anxiety_general.csv @@ -6007,7 +6043,7 @@ actions: model_output: output/model_output-cohort_vax-sub_sex_male-anxiety_general.csv make_model_input-cohort_vax-sub_sex_male-depression: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_sex_male-depression + run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_male-depression needs: - stage1_data_cleaning_all outputs: @@ -6017,7 +6053,7 @@ actions: cox_ipw-cohort_vax-sub_sex_male-depression: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_sex_male-depression.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_male-depression.csv @@ -6028,7 +6064,7 @@ actions: model_output: output/model_output-cohort_vax-sub_sex_male-depression.csv make_model_input-cohort_vax-sub_sex_male-serious_mental_illness: - run: r:latest analysis/model/make_model_input.R cohort_vax-sub_sex_male-serious_mental_illness + run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_male-serious_mental_illness needs: - stage1_data_cleaning_all outputs: @@ -6038,7 +6074,7 @@ actions: cox_ipw-cohort_vax-sub_sex_male-serious_mental_illness: run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_sex_male-serious_mental_illness.rds --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm + --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_male-serious_mental_illness.csv @@ -6048,250 +6084,3 @@ actions: moderately_sensitive: model_output: output/model_output-cohort_vax-sub_sex_male-serious_mental_illness.csv - ## Stage 6 - make model output - - make_model_output: - run: r:latest analysis/model/make_model_output.R - needs: - - cox_ipw-cohort_prevax-main-addiction - - cox_ipw-cohort_prevax-sub_covid_hospitalised-addiction - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-addiction - - cox_ipw-cohort_vax-main-addiction - - cox_ipw-cohort_vax-sub_covid_hospitalised-addiction - - cox_ipw-cohort_vax-sub_covid_nonhospitalised-addiction - - cox_ipw-cohort_vax-sub_covid_history-addiction - - cox_ipw-cohort_unvax-main-addiction - - cox_ipw-cohort_unvax-sub_covid_hospitalised-addiction - - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-addiction - - cox_ipw-cohort_unvax-sub_covid_history-addiction - - cox_ipw-cohort_prevax-main-anxiety_general - - cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_general - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_general - - cox_ipw-cohort_prevax-sub_priorhistory_none-anxiety_general - - cox_ipw-cohort_prevax-sub_priorhistory_recent-anxiety_general - - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-anxiety_general - - cox_ipw-cohort_prevax-sub_sex_female-anxiety_general - - cox_ipw-cohort_prevax-sub_sex_male-anxiety_general - - cox_ipw-cohort_prevax-sub_age_18_39-anxiety_general - - cox_ipw-cohort_prevax-sub_age_40_59-anxiety_general - - cox_ipw-cohort_prevax-sub_age_60_79-anxiety_general - - cox_ipw-cohort_prevax-sub_age_80_110-anxiety_general - - cox_ipw-cohort_prevax-sub_ethnicity_white-anxiety_general - - cox_ipw-cohort_prevax-sub_ethnicity_black-anxiety_general - - cox_ipw-cohort_prevax-sub_ethnicity_mixed-anxiety_general - - cox_ipw-cohort_prevax-sub_ethnicity_asian-anxiety_general - - cox_ipw-cohort_prevax-sub_ethnicity_other-anxiety_general - - cox_ipw-cohort_vax-main-anxiety_general - - cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_general - - cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_general - - cox_ipw-cohort_vax-sub_covid_history-anxiety_general - - cox_ipw-cohort_vax-sub_priorhistory_none-anxiety_general - - cox_ipw-cohort_vax-sub_priorhistory_recent-anxiety_general - - cox_ipw-cohort_vax-sub_priorhistory_notrecent-anxiety_general - - cox_ipw-cohort_vax-sub_sex_female-anxiety_general - - cox_ipw-cohort_vax-sub_sex_male-anxiety_general - - cox_ipw-cohort_vax-sub_age_18_39-anxiety_general - - cox_ipw-cohort_vax-sub_age_40_59-anxiety_general - - cox_ipw-cohort_vax-sub_age_60_79-anxiety_general - - cox_ipw-cohort_vax-sub_age_80_110-anxiety_general - - cox_ipw-cohort_vax-sub_ethnicity_white-anxiety_general - - cox_ipw-cohort_vax-sub_ethnicity_black-anxiety_general - - cox_ipw-cohort_vax-sub_ethnicity_mixed-anxiety_general - - cox_ipw-cohort_vax-sub_ethnicity_asian-anxiety_general - - cox_ipw-cohort_vax-sub_ethnicity_other-anxiety_general - - cox_ipw-cohort_unvax-main-anxiety_general - - cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_general - - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_general - - cox_ipw-cohort_unvax-sub_covid_history-anxiety_general - - cox_ipw-cohort_unvax-sub_priorhistory_none-anxiety_general - - cox_ipw-cohort_unvax-sub_priorhistory_recent-anxiety_general - - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-anxiety_general - - cox_ipw-cohort_unvax-sub_sex_female-anxiety_general - - cox_ipw-cohort_unvax-sub_sex_male-anxiety_general - - cox_ipw-cohort_unvax-sub_age_18_39-anxiety_general - - cox_ipw-cohort_unvax-sub_age_40_59-anxiety_general - - cox_ipw-cohort_unvax-sub_age_60_79-anxiety_general - - cox_ipw-cohort_unvax-sub_age_80_110-anxiety_general - - cox_ipw-cohort_unvax-sub_ethnicity_white-anxiety_general - - cox_ipw-cohort_unvax-sub_ethnicity_black-anxiety_general - - cox_ipw-cohort_unvax-sub_ethnicity_mixed-anxiety_general - - cox_ipw-cohort_unvax-sub_ethnicity_asian-anxiety_general - - cox_ipw-cohort_unvax-sub_ethnicity_other-anxiety_general - - cox_ipw-cohort_prevax-main-anxiety_ptsd - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd - - cox_ipw-cohort_vax-main-anxiety_ptsd - - cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_ptsd - - cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd - - cox_ipw-cohort_vax-sub_covid_history-anxiety_ptsd - - cox_ipw-cohort_unvax-main-anxiety_ptsd - - cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd - - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd - - cox_ipw-cohort_unvax-sub_covid_history-anxiety_ptsd - - cox_ipw-cohort_prevax-main-depression - - cox_ipw-cohort_prevax-sub_covid_hospitalised-depression - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-depression - - cox_ipw-cohort_prevax-sub_priorhistory_none-depression - - cox_ipw-cohort_prevax-sub_priorhistory_recent-depression - - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-depression - - cox_ipw-cohort_prevax-sub_sex_female-depression - - cox_ipw-cohort_prevax-sub_sex_male-depression - - cox_ipw-cohort_prevax-sub_age_18_39-depression - - cox_ipw-cohort_prevax-sub_age_40_59-depression - - cox_ipw-cohort_prevax-sub_age_60_79-depression - - cox_ipw-cohort_prevax-sub_age_80_110-depression - - cox_ipw-cohort_prevax-sub_ethnicity_white-depression - - cox_ipw-cohort_prevax-sub_ethnicity_black-depression - - cox_ipw-cohort_prevax-sub_ethnicity_mixed-depression - - cox_ipw-cohort_prevax-sub_ethnicity_asian-depression - - cox_ipw-cohort_prevax-sub_ethnicity_other-depression - - cox_ipw-cohort_vax-main-depression - - cox_ipw-cohort_vax-sub_covid_hospitalised-depression - - cox_ipw-cohort_vax-sub_covid_nonhospitalised-depression - - cox_ipw-cohort_vax-sub_covid_history-depression - - cox_ipw-cohort_vax-sub_priorhistory_none-depression - - cox_ipw-cohort_vax-sub_priorhistory_recent-depression - - cox_ipw-cohort_vax-sub_priorhistory_notrecent-depression - - cox_ipw-cohort_vax-sub_sex_female-depression - - cox_ipw-cohort_vax-sub_sex_male-depression - - cox_ipw-cohort_vax-sub_age_18_39-depression - - cox_ipw-cohort_vax-sub_age_40_59-depression - - cox_ipw-cohort_vax-sub_age_60_79-depression - - cox_ipw-cohort_vax-sub_age_80_110-depression - - cox_ipw-cohort_vax-sub_ethnicity_white-depression - - cox_ipw-cohort_vax-sub_ethnicity_black-depression - - cox_ipw-cohort_vax-sub_ethnicity_mixed-depression - - cox_ipw-cohort_vax-sub_ethnicity_asian-depression - - cox_ipw-cohort_vax-sub_ethnicity_other-depression - - cox_ipw-cohort_unvax-main-depression - - cox_ipw-cohort_unvax-sub_covid_hospitalised-depression - - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-depression - - cox_ipw-cohort_unvax-sub_covid_history-depression - - cox_ipw-cohort_unvax-sub_priorhistory_none-depression - - cox_ipw-cohort_unvax-sub_priorhistory_recent-depression - - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-depression - - cox_ipw-cohort_unvax-sub_sex_female-depression - - cox_ipw-cohort_unvax-sub_sex_male-depression - - cox_ipw-cohort_unvax-sub_age_18_39-depression - - cox_ipw-cohort_unvax-sub_age_40_59-depression - - cox_ipw-cohort_unvax-sub_age_60_79-depression - - cox_ipw-cohort_unvax-sub_age_80_110-depression - - cox_ipw-cohort_unvax-sub_ethnicity_white-depression - - cox_ipw-cohort_unvax-sub_ethnicity_black-depression - - cox_ipw-cohort_unvax-sub_ethnicity_mixed-depression - - cox_ipw-cohort_unvax-sub_ethnicity_asian-depression - - cox_ipw-cohort_unvax-sub_ethnicity_other-depression - - cox_ipw-cohort_prevax-main-eating_disorders - - cox_ipw-cohort_prevax-sub_covid_hospitalised-eating_disorders - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-eating_disorders - - cox_ipw-cohort_prevax-main-self_harm - - cox_ipw-cohort_prevax-sub_covid_hospitalised-self_harm - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-self_harm - - cox_ipw-cohort_vax-main-self_harm - - cox_ipw-cohort_vax-sub_covid_hospitalised-self_harm - - cox_ipw-cohort_vax-sub_covid_nonhospitalised-self_harm - - cox_ipw-cohort_vax-sub_covid_history-self_harm - - cox_ipw-cohort_unvax-main-self_harm - - cox_ipw-cohort_unvax-sub_covid_hospitalised-self_harm - - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-self_harm - - cox_ipw-cohort_unvax-sub_covid_history-self_harm - - cox_ipw-cohort_prevax-main-serious_mental_illness - - cox_ipw-cohort_prevax-sub_covid_hospitalised-serious_mental_illness - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness - - cox_ipw-cohort_prevax-sub_priorhistory_none-serious_mental_illness - - cox_ipw-cohort_prevax-sub_priorhistory_recent-serious_mental_illness - - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness - - cox_ipw-cohort_prevax-sub_sex_female-serious_mental_illness - - cox_ipw-cohort_prevax-sub_sex_male-serious_mental_illness - - cox_ipw-cohort_prevax-sub_age_18_39-serious_mental_illness - - cox_ipw-cohort_prevax-sub_age_40_59-serious_mental_illness - - cox_ipw-cohort_prevax-sub_age_60_79-serious_mental_illness - - cox_ipw-cohort_prevax-sub_age_80_110-serious_mental_illness - - cox_ipw-cohort_prevax-sub_ethnicity_white-serious_mental_illness - - cox_ipw-cohort_prevax-sub_ethnicity_black-serious_mental_illness - - cox_ipw-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness - - cox_ipw-cohort_prevax-sub_ethnicity_asian-serious_mental_illness - - cox_ipw-cohort_prevax-sub_ethnicity_other-serious_mental_illness - - cox_ipw-cohort_vax-main-serious_mental_illness - - cox_ipw-cohort_vax-sub_covid_hospitalised-serious_mental_illness - - cox_ipw-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness - - cox_ipw-cohort_vax-sub_covid_history-serious_mental_illness - - cox_ipw-cohort_vax-sub_priorhistory_none-serious_mental_illness - - cox_ipw-cohort_vax-sub_priorhistory_recent-serious_mental_illness - - cox_ipw-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness - - cox_ipw-cohort_vax-sub_sex_female-serious_mental_illness - - cox_ipw-cohort_vax-sub_sex_male-serious_mental_illness - - cox_ipw-cohort_vax-sub_age_18_39-serious_mental_illness - - cox_ipw-cohort_vax-sub_age_40_59-serious_mental_illness - - cox_ipw-cohort_vax-sub_age_60_79-serious_mental_illness - - cox_ipw-cohort_vax-sub_age_80_110-serious_mental_illness - - cox_ipw-cohort_vax-sub_ethnicity_white-serious_mental_illness - - cox_ipw-cohort_vax-sub_ethnicity_black-serious_mental_illness - - cox_ipw-cohort_vax-sub_ethnicity_mixed-serious_mental_illness - - cox_ipw-cohort_vax-sub_ethnicity_asian-serious_mental_illness - - cox_ipw-cohort_vax-sub_ethnicity_other-serious_mental_illness - - cox_ipw-cohort_unvax-main-serious_mental_illness - - cox_ipw-cohort_unvax-sub_covid_hospitalised-serious_mental_illness - - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness - - cox_ipw-cohort_unvax-sub_covid_history-serious_mental_illness - - cox_ipw-cohort_unvax-sub_priorhistory_none-serious_mental_illness - - cox_ipw-cohort_unvax-sub_priorhistory_recent-serious_mental_illness - - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness - - cox_ipw-cohort_unvax-sub_sex_female-serious_mental_illness - - cox_ipw-cohort_unvax-sub_sex_male-serious_mental_illness - - cox_ipw-cohort_unvax-sub_age_18_39-serious_mental_illness - - cox_ipw-cohort_unvax-sub_age_40_59-serious_mental_illness - - cox_ipw-cohort_unvax-sub_age_60_79-serious_mental_illness - - cox_ipw-cohort_unvax-sub_age_80_110-serious_mental_illness - - cox_ipw-cohort_unvax-sub_ethnicity_white-serious_mental_illness - - cox_ipw-cohort_unvax-sub_ethnicity_black-serious_mental_illness - - cox_ipw-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness - - cox_ipw-cohort_unvax-sub_ethnicity_asian-serious_mental_illness - - cox_ipw-cohort_unvax-sub_ethnicity_other-serious_mental_illness - - cox_ipw-cohort_prevax-main-suicide - - cox_ipw-cohort_prevax-sub_covid_hospitalised-suicide - - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-suicide - outputs: - moderately_sensitive: - model_output: output/model_output.csv - - ## Temp - - cox_ipw-cohort_prevax-main-depression-v0.0.9: - run: cox-ipw:v0.0.9 --df_input=model_input-cohort_prevax-main-depression.rds --ipw=TRUE - --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18 - --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-depression-v0.0.9.csv - needs: - - make_model_input-cohort_prevax-main-depression - outputs: - moderately_sensitive: - model_output: output/model_output-cohort_prevax-main-depression-v0.0.9.csv - - cox_ipw-cohort_vax-main-depression-v0.0.9: - run: cox-ipw:v0.0.9 --df_input=model_input-cohort_vax-main-depression.rds --ipw=TRUE - --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 - --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-depression-v0.0.9 - needs: - - make_model_input-cohort_vax-main-depression - outputs: - moderately_sensitive: - model_output: output/model_output-cohort_vax-main-depression-v0.0.9.csv - - cox_ipw-cohort_unvax-main-depression-v0.0.9: - run: cox-ipw:v0.0.9 --df_input=model_input-cohort_unvax-main-depression.rds --ipw=FALSE - --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex - --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm - --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14 - --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5 - --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-depression-v0.0.9 - needs: - - make_model_input-cohort_unvax-main-depression - outputs: - moderately_sensitive: - model_output: output/model_output-cohort_unvax-main-depression-v0.0.9.csv -